DocumentationList of modules
Complete module table
A , B , C , D , E , F , G , H , I , J , K , L , M , N , O , P , Q , R , S , T , U , V , W , X , Y , Z
3
| module name | link to docs | description |
|---|---|---|
| 3d-dna |
A
| module name | link to docs | description |
|---|---|---|
| abcranger | ||
| abinit | abinit | ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. |
| abyss | abyss | |
| act | ||
| adios2 | The Adaptable Input Output System version 2, developed in the Exascale Computing Program | |
| admixture | ||
| ale | ||
| allhic | ||
| allineaddt | ||
| alpine | ||
| alsa-lib | The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib contains the user space library that developers compile ALSA applications against. | |
| amber | amber | |
| amos | ||
| anaconda3 | ||
| angsd | ||
| ansys | ansys | |
| ant | Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other | |
| antismash | ||
| ants | ||
| any2fasta | ||
| aocc-compiler | loads AOCC compiler setup | |
| aocc | The AOCC compiler system is a high performance, production quality code generation tool. The AOCC environment provides various options to developers when building and optimizing C, C++, and Fortran applications targeting 32-bit and 64-bit Linux platforms. The AOCC compiler system offers a high level of advanced optimizations, multi-threading and processor support that includes global optimization, vectorization, inter-procedural analyses, loop transformations, and code generation. AMD also provides highly optimized libraries, which extract the optimal performance from each x86 processor core when utilized. The AOCC Compiler Suite simplifies and accelerates development and tuning for x86 applications. Please install only if you agree to terms and conditions depicted under : http://developer.amd.com/wordpress/media/files/AOCC_EULA.pdf Example for installation: spack install aocc +license-agreed | |
| aom | Alliance for Open Media AOM AV1 Codec Library | |
| apr-util | Apache Portable Runtime Utility | |
| apr | Apache portable runtime. | |
| arcs | ||
| argtable | Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. | |
| aria2 | ||
| armadillo | Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use. | |
| arpack-ng | ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. | |
| arrayfire | ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming more accessible. | |
| arrow | A cross-language development platform for in-memory data. | |
| artemis | ||
| ase | ||
| aspera-cli | The Aspera CLI client for the Fast and Secure Protocol (FASP). | |
| aspera-connect | The Aspera Connect client for the Fast and Secure Protocol (FASP). | |
| assimp | Open Asset Import Library (Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner. | |
| astral | ||
| at-spi2-atk | The At-Spi2 Atk package contains a library that bridges ATK to At-Spi2 D-Bus service. | |
| at-spi2-core | The At-Spi2 Core package provides a Service Provider Interface for the Assistive Technologies available on the GNOME platform and a library against which applications can be linked. | |
| atk | ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. | |
| atlas | ||
| atompaw | A Projector Augmented Wave (PAW) code for generating atom-centered functions. | |
| atram | ||
| augustus | augustus | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences |
| autoconf-archive | The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf. | |
| autoconf | Autoconf — system configuration part of autotools | |
| autodock | ||
| autogrow | ||
| automake | Automake — make file builder part of autotools | |
| autotools | ||
| avogadro |
B
| module name | link to docs | description |
|---|---|---|
| babel | ||
| baitfisher | BaitFisher was been designed to construct hybrid enrichment baits from multiple sequence alignments (MSAs) or annotated features in MSAs. | |
| bam2fastq | ||
| bamqc | ||
| bamtools | C++ API command-line toolkit for working with BAM data. | |
| bayescan | ||
| bayesembler | Bayesian method for doing transcriptome assembly from RNA-seq data | |
| bazel | Bazel is an open-source build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users. | |
| bbmap | Short read aligner for DNA and RNA-seq data. | |
| bc | bc is an arbitrary precision numeric processing language. Syntax is similar to C, but differs in many substantial areas. It supports interactive execution of statements. | |
| bcftools | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. | |
| bcl2fastq2 | ||
| bdftopcf | bdftopcf is a font compiler for the X server and font server. Fonts in Portable Compiled Format can be read by any architecture, although the file is structured to allow one particular architecture to read them directly without reformatting. This allows fast reading on the appropriate machine, but the files are still portable (but read more slowly) on other machines. | |
| bdw-gc | The Boehm-Demers-Weiser conservative garbage collector is a garbage collecting replacement for C malloc or C++ new. | |
| beast | beast | |
| beast2 | BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. | |
| bedops | ||
| bedtools | ||
| bedtools2 | Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. | |
| berkeley-db | Oracle Berkeley DB | |
| berkeleygw | BerkeleyGW is a many-body perturbation theory code for excited states, using the GW method and the GW plus Bethe-Salpeter equation (GW-BSE) method to solve respectively for quasiparticle excitations and optical properties of materials. | |
| binutils | GNU binutils, which contain the linker, assembler, objdump and others | |
| bioperl | ||
| bismark | ||
| bison | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. | |
| blasr-libcpp | Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. | |
| blasr | The PacBio long read aligner. | |
| blast-plus | Basic Local Alignment Search Tool. | |
| blast | blast | |
| blastfoam | ||
| blat-suite | ||
| blender | ||
| blobtools | ||
| boost | Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. | |
| bowtie | Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. | |
| bowtie2 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences | |
| bpp-core | Bio++ core library. | |
| bpp-seq | Bio++ seq library. | |
| braker | BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS | |
| braker2 | ||
| bridger | ||
| bucky | ||
| busco | busco | |
| bwa-mem2 | Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. | |
| bwa | bwa | |
| bzip2 | bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10 to 15 of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. |
C
| module name | link to docs | description |
|---|---|---|
| c-ares | c-ares: A C library for asynchronous DNS requests | |
| c-blosc | Blosc, an extremely fast, multi-threaded, meta-compressor library | |
| cactus | ||
| caffe2016 | ||
| cairo | Cairo is a 2D graphics library with support for multiple output devices. | |
| canu | canu | |
| cap3 | ||
| capnproto | ||
| cc4s | ||
| ccmetagen | ||
| ccp4 | ||
| cdbfasta | Fast indexing and retrieval of fasta records from flat file databases | |
| cdhit | CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. | |
| cdo | ||
| cellprofiler | ||
| cellranger | ||
| cem | CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads | |
| cereal | cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. | |
| cfitsio | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. | |
| cfour | ||
| cgal | The Computational Geometry Algorithms Library (CGAL) is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics. | |
| cgns | The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data. | |
| charmm | ||
| charmpp | Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers. | |
| chimera | ||
| chromevol | ||
| cicero | ||
| circos | ||
| clang | ||
| clcgenomicswb | ||
| clhep | CLHEP is a C++ Class Library for High Energy Physics. | |
| cli11 | CLI11 is a command line parser for C++11 and beyond that provides a rich feature set with a simple and intuitive interface. | |
| clingo | Clingo: A grounder and solver for logic programs | |
| clp | Clp (Coin-or linear programming) is an open-source linear programming solver written in C++. | |
| clustal-omega | ||
| clustal-wx | ||
| clview | ||
| cmake | A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. | |
| cmdstan | CmdStan is the command line interface to Stan. | |
| coinutils | CoinUtils is an open-source collection of classes and helper functions that are generally useful to multiple COIN-OR projects. | |
| colabfold | ||
| columbus | ||
| conda-modules | conda-modules | |
| consemble | ||
| consent | ||
| coreutils | The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. | |
| cosma | Distributed Communication-Optimal Matrix-Matrix Multiplication Library | |
| cp2k | cp2k | CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems |
| cpio | GNU cpio copies files into or out of a cpio or tar archive and the file system. The archive can be another file on the disk, a magnetic tape, or a pipe. | |
| cplex | cplex | |
| cryosparc | ||
| cryptopp | Crypto++ is an open-source C++ library of cryptographic schemes. The library supports a number of different cryptography algorithms, including authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2), public-key encryption (RSA, DSA), and a few obsolete/historical encryption algorithms (MD5, Panama). | |
| crystal | ||
| ctk | ||
| cuda | cuda | CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). |
| cudnn | cudnn | NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks |
| cufflinks | cufflinks | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. |
| cups | CUPS is the standards-based, open source printing system developed by Apple Inc. for macOS and other UNIX-like operating systems. CUPS uses the Internet Printing Protocol (IPP) to support printing to local and network printers. This provides the core CUPS libraries, not a complete CUPS install. | |
| curl | cURL is an open source command line tool and library for transferring data with URL syntax | |
| cyrus-sasl | This is the Cyrus SASL API implementation. It can be used on the client or server side to provide authentication and authorization services. |
D
| module name | link to docs | description |
|---|---|---|
| daccor | ||
| dakota | ||
| dalton | The Dalto nprogram is designed to allow convenient, automated determination of a largenumber of molecular properties based on an HF, HF-srDFT, DFT, MP2, CC, CI, MCSCF or MC-srDFT reference wave function. | |
| damageproto | X Damage Extension. | |
| dataanalysis | ||
| datamash | ||
| davix | High-performance file management over WebDAV/HTTP. | |
| dbus | D-Bus is a message bus system, a simple way for applications to talk to one another. D-Bus supplies both a system daemon (for events such new hardware device printer queue ) and a per-user-login-session daemon (for general IPC needs among user applications). Also, the message bus is built on top of a general one-to-one message passing framework, which can be used by any two applications to communicate directly (without going through the message bus daemon). | |
| ddocent | ||
| debian7 | ||
| debian8 | ||
| debian9 | ||
| debian10 | ||
| debian11 | ||
| desmond | desmond | |
| detonate | ||
| dftbplus | ||
| dftd4 | Generally Applicable Atomic-Charge Dependent London Dispersion Correction | |
| diamond | DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. | |
| diffutils | GNU Diffutils is a package of several programs related to finding differences between files. | |
| dirac | dirac | Dirac is Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations |
| diyabc | ||
| dmacrys | ||
| dmnrg | ||
| dnapipete | ||
| docbook-xml | Docbook DTD XML files. | |
| docbook-xsl | DocBook XSLT 1.0 Stylesheets. | |
| dock | ||
| dotnet | ||
| double-conversion | This project (double-conversion) provides binary-decimal and decimal-binary routines for IEEE doubles. | |
| doxygen | Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D.. | |
| dssp | ||
| duplextools |
E
| module name | link to docs | description |
|---|---|---|
| eccodes | ecCodes is a package developed by ECMWF for processing meteorological data in GRIB (1/2), BUFR (3/4) and GTS header formats. | |
| ed | GNU ed is a line-oriented text editor. It is used to create, display, modify and otherwise manipulate text files, both interactively and via shell scripts. | |
| edena | ||
| edirect | ||
| eigen | Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms. | |
| elk | ||
| elpa | Eigenvalue solvers for Petaflop-Applications (ELPA) | |
| emboss | ||
| endhic | ||
| entrezdirect | Entrez Direct (EDirect) provides access to the NCBIs suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. | |
| entropy | ||
| erne | The Extended Randomized Numerical alignEr using BWT | |
| esm-rism_q | ||
| espresso | ||
| espresso_md | ||
| ete-toolkit | ||
| exabayes | ||
| examl | ||
| exonerate | exonerate | Pairwise sequence alignment of DNA and proteins |
| expat | Expat is an XML parser library written in C. | |
| expect | Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. | |
| express | eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. |
F
| module name | link to docs | description |
|---|---|---|
| fasta | The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. | |
| fastme | FastME is a distance based phylogeny reconstruction program that works on distance matrices and, as of v2.0, sequence data. | |
| fastp | A tool designed to provide fast all-in-one preprocessing for FastQ files. | |
| fastq-pair | ||
| fastq_illumina_filter | ||
| fastqc | A quality control tool for high throughput sequence data. | |
| fastqscreen | ||
| fastqvalidator | ||
| fastsimcoal2 | ||
| faststructure | faststructure | |
| fasttree | ||
| fastuniq | ||
| fastx | ||
| fcgi | FastCGI is simple because it is actually CGI with only a few extensions. Like CGI, FastCGI is also language-independent. For instance, FastCGI provides a way to improve the performance of the thousands of Perl applications that have been written for the Web. | |
| fenics | ||
| ffmpeg | FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. | |
| fftw | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. | |
| fhi-aims | ||
| fiji | ||
| file | The file command is a file type guesser, that is, a command-line tool that tells you in words what kind of data a file contains | |
| filesender | ||
| filtlong | ||
| findutils | The GNU Find Utilities are the basic directory searching utilities of the GNU operating system. | |
| fineradstructure | ||
| fixesproto | X Fixes Extension. | |
| flash | ||
| flatbuffers | Memory Efficient Serialization Library | |
| flex | Flex is a tool for generating scanners. | |
| flexbar | ||
| fltk | FLTK (pronounced fulltick) is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. | |
| flye | ||
| fmt | fmt (formerly cppformat) is an open-source formatting library. It can be used as a safe alternative to printf or as a fast alternative to C++ IOStreams. | |
| font-util | X.Org font package creation/installation utilities and fonts. | |
| fontconfig | Fontconfig is a library for configuring/customizing font access | |
| fontsproto | X Fonts Extension. | |
| fpm | Fortran Package Manager (fpm) is a package manager and build system for Fortran. Its key goal is to improve the user experience of Fortran programmers. It does so by making it easier to build your Fortran program or library, run the executables, tests, and examples, and distribute it as a dependency to other Fortran projects. | |
| freebayes | ||
| freeglut | FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library | |
| freesurfer | freesurfer | |
| freetype | FreeType is a freely available software library to render fonts. It is written in C, designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images) of most vector and bitmap font formats. | |
| fribidi | GNU FriBidi: The Free Implementation of the Unicode Bidirectional Algorithm. | |
| fsl | fsl | |
| ftgl | Library to use arbitrary fonts in OpenGL applications. | |
| fyba | OpenFYBA is the source code release of the FYBA library, distributed by the National Mapping Authority of Norway (Statens kartverk) to read and write files in the National geodata standard format SOSI. |
G
| module name | link to docs | description |
|---|---|---|
| g03 | ||
| g4abla | Geant4 data for nuclear shell effects in INCL/ABLA hadronic mode | |
| g4emlow | Geant4 data files for low energy electromagnetic processes. | |
| g4ensdfstate | Geant4 data for nuclides properties | |
| g4incl | Geant4 data for evaluated particle cross-sections on natural composition of elements | |
| g4ndl | Geant4 Neutron data files with thermal cross sections | |
| g4particlexs | Geant4 data for evaluated particle cross-sections on natural composition of elements | |
| g4photonevaporation | Geant4 data for photon evaporation | |
| g4pii | Geant4 data for shell ionisation cross-sections | |
| g4radioactivedecay | Geant4 data files for radio-active decay hadronic processes | |
| g4realsurface | Geant4 data for measured optical surface reflectance | |
| g4saiddata | Geant4 data from evaluated cross-sections in SAID data-base | |
| g09 | ||
| g16 | ||
| gamess | gamess | |
| gapcloser | The GapCloser is designed to close the gaps emerging during the scaffolding process | |
| gate | ||
| gatk | gatk | Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data |
| gawk | If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. To write a program to do this in a language such as C or Pascal is a time-consuming inconvenience that may take many lines of code. The job is easy with awk, especially the GNU implementation: gawk. | |
| gcc | gcc | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. |
| gdal | GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing. | |
| gdbm | GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database. | |
| gdk-pixbuf | The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. | |
| gdma | ||
| gdrcopy | A fast GPU memory copy library based on NVIDIA GPUDirect RDMA technology. | |
| geant4-data | A bundle package to hold Geant4 data packages | |
| geant4 | Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. | |
| geneious | geneious | |
| genemark-et | Gene Prediction in Bacteria, archaea, Metagenomes and Metatranscriptomes. When downloaded this file is named the same for all versions. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html | |
| genemark | ||
| genespace | ||
| genomethreader | ||
| genometools | genometools is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. | |
| genrich | Genrich is a peak-caller for genomic enrichment assays. | |
| geos | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions. | |
| gettext | GNU internationalization (i18n) and localization (l10n) library. | |
| gffcompare | ||
| gffread | ||
| ghostscript-fonts | Ghostscript Fonts | |
| ghostscript | An interpreter for the PostScript language and for PDF. | |
| gibpss | gibpss | |
| giflib | The GIFLIB project maintains the giflib service library, which has been pulling images out of GIFs since 1989. | |
| git-lfs | Git LFS is a system for managing and versioning large files in association with a Git repository. Instead of storing the large files within the Git repository as blobs, Git LFS stores special pointer files in the repository, while storing the actual file contents on a Git LFS server. | |
| git | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. | |
| gl2ps | GL2PS is a C library providing high quality vector output for any OpenGL application. | |
| glapd | ||
| glew | The OpenGL Extension Wrangler Library. | |
| glib | GLib provides the core application building blocks for libraries and applications written in C. | |
| glibc | ||
| glimmerhmm | ||
| globalarrays | Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency. | |
| glpk | The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. | |
| glproto | OpenGL Extension to the X Window System. | |
| gmake | GNU Make is a tool which controls the generation of executables and other non-source files of a program from the programs source files. | |
| gmap | ||
| gmp | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. | |
| gnuplot | Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you dont have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986 | |
| gnutls | GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS 12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability. | |
| go-bootstrap | Old C-bootstrapped go to bootstrap real go | |
| go | The golang compiler and build environment | |
| gobject-introspection | The GObject Introspection is used to describe the program APIs and collect them in a uniform, machine readable format.Cairo is a 2D graphics library with support for multiple output | |
| google-crc32c | CRC32C implementation with support for CPU-specific acceleration instructions. | |
| googletest | Google test framework for C++. Also called gtest. | |
| gpaw | ||
| gperf | GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. | |
| gperftools | ||
| gphocs | ||
| grace | ||
| gradle | ||
| graphite2 | Graphite is a system that can be used to create smart fonts capable of displaying writing systems with various complex behaviors. A smart font contains not only letter shapes but also additional instructions indicating how to combine and position the letters in complex ways. | |
| graphmap | ||
| graphviz | Graph Visualization Software | |
| gridmathematica | gridmathematica | |
| groff | Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. Output may be PostScript or PDF, html, or ASCII/UTF8 for display at the terminal. | |
| gromacs | GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. | |
| gsl | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite. | |
| gstreamer | ||
| gtk-doc | GtkDoc is a tool used to extract API documentation from C-code like Doxygen, but handles documentation of GObject (including signals and properties) that makes it very suitable for GTK+ apps and libraries. It uses docbook for intermediate files and can produce html by default and pdf/man-pages with some extra work. | |
| gtkplus | The GTK+ package contains libraries used for creating graphical user interfaces for applications. | |
| gts | GTS stands for the GNU Triangulated Surface Library. | |
| gui | ||
| guidance | ||
| guile | Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. | |
| guppy | guppy | |
| gzip | GNU Gzip is a popular data compression program originally written by Jean-loup Gailly for the GNU project. |
H
| module name | link to docs | description |
|---|---|---|
| hamstr | ||
| hapcut2 | ||
| harfbuzz | The Harfbuzz package contains an OpenType text shaping engine. | |
| hdf | HDF4 (also known as HDF) is a library and multi-object file format for storing and managing data between machines. | |
| hdf5 | HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. | |
| helm | ||
| help2man | help2man produces simple manual pages from the —help and —version output of other commands. | |
| hicpro | ||
| highfive | HighFive - Header only C++ HDF5 interface | |
| hisat | ||
| hisat2 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome). | |
| hmmer | HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). | |
| htk | ||
| htscodecs | Custom CRAM codecs used for EXTERNAL block types. | |
| htseq | ||
| htslib | C library for high-throughput sequencing data formats. | |
| huygens | ||
| hwloc | The Hardware Locality (hwloc) software project. | |
| hyperqueue | Scheduler for sub-node tasks for HPC systems with batch scheduling | |
| hyphy |
I
| module name | link to docs | description |
|---|---|---|
| icu4c | ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU4C is the C/C++ interface. | |
| idv | ||
| igraph | ||
| imagemagick | ImageMagick is a software suite to create, edit, compose, or convert bitmap images. | |
| imake | The imake build system. | |
| inputproto | X Input Extension. | |
| intel-mkl | Intel Math Kernel Library. | |
| intel-oneapi-advisor | Intel oneAPI advisor 2025.4.0 | |
| intel-oneapi-ccl | Intel oneAPI ccl 2021.17 | |
| intel-oneapi-compiler | Intel oneAPI compiler 2025.3 | |
| intel-oneapi-compilers | Intel oneAPI Compiler 2025.1.1 (DPC++, ICX, IFX, IFORT) | |
| intel-oneapi-dal | Intel oneAPI dal 2025.9 | |
| intel-oneapi-debugger | Intel oneAPI debugger 2025.3 | |
| intel-oneapi-dnnl | Intel oneAPI dnnl 2025.3 | |
| intel-oneapi-hpc-compilers | Intel oneAPI compiler 2025.1.1 | |
| intel-oneapi-ipp | Intel oneAPI ipp 2022.3 | |
| intel-oneapi-ippcp | Intel oneAPI ippcp 2025.1 | |
| intel-oneapi-ishmem | Intel oneAPI SHMEM Library 1.3 | |
| intel-oneapi-mkl | Intel oneAPI mkl 2025.3 | |
| intel-oneapi-mpi | Intel oneAPI MPI Library 2021.15 | |
| intel-oneapi-tbb | Intel oneAPI tbb 2022.3 | |
| intel-oneapi-vtune | Intel oneAPI vtune 2025.7 | |
| intel-parallel-studio | Intel Parallel Studio. | |
| intel-tbb | Widely used C++ template library for task parallelism. Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability. | |
| intelcdk | ||
| intelmpi | ||
| interproscan | interproscan | |
| intltool | intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. | |
| iqtree | ||
| irys | ||
| isl | isl (Integer Set Library) is a thread-safe C library for manipulating sets and relations of integer points bounded by affine constraints. | |
| itk | ||
| itstool | ITS Tool allows you to translate your XML documents with PO files, using rules from the W3C Internationalization Tag Set (ITS) to determine what to translate and how to separate it into PO file messages. |
J
| module name | link to docs | description |
|---|---|---|
| jasper | Library for manipulating JPEG-2000 images | |
| java3d | ||
| jbigkit | JBIG-Kit is a software implementation of the JBIG1 data compression standard. | |
| jdk | ||
| jdkibm | ||
| jellyfish | ||
| jemalloc | jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. | |
| jmodeltest | ||
| json-c | A JSON implementation in C. | |
| jsoncpp | JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. | |
| julia | julia | The Julia Language: A fresh approach to technical computing |
| jupyter-modules | ||
| jvarkit |
K
| module name | link to docs | description |
|---|---|---|
| kahip | KaHIP - Karlsruhe High Quality Partitioning - is a family of graph partitioning programs. It includes KaFFPa (Karlsruhe Fast Flow Partitioner), which is a multilevel graph partitioning algorithm, in its variants Strong, Eco and Fast, KaFFPaE (KaFFPaEvolutionary) which is a parallel evolutionary algorithm that uses KaFFPa to provide combine and mutation operations, as well as KaBaPE which extends the evolutionary algorithm. Moreover, specialized techniques are included to partition road networks (Buffoon), to output a vertex separator from a given partition or techniques geared towards efficient partitioning of social networks. | |
| kallisto | kallisto is a program for quantifying abundances of transcripts from RNA-Seq data. | |
| kat | ||
| kbproto | X Keyboard Extension. | |
| kealib | An HDF5 Based Raster File Format. | |
| keyutils | These tools are used to control the key management system built into the Linux kernel. | |
| kim-api | OpenKIM is an online framework for making molecular simulations reliable, reproducible, and portable. Computer implementations of inter-atomic models are archived in OpenKIM, verified for coding integrity, and tested by computing their predictions for a variety of material properties. Models conforming to the KIM application programming interface (API) work seamlessly with major simulation codes that have adopted the KIM API standard. | |
| kma | ||
| kmc | ||
| knem | KNEM is a Linux kernel module enabling high-performance intra-node MPI communication for large messages. | |
| kokkos | Kokkos implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. | |
| kraken | kraken | |
| kraken2 | ||
| krb5 | Network authentication protocol | |
| krona | ||
| kubectl |
L
| module name | link to docs | description |
|---|---|---|
| lam | ||
| lame | LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. | |
| lammps | lammps | LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion. |
| last | ||
| lastz | ||
| latte | Open source density functional tight binding molecular dynamics. | |
| lcms | Little cms is a color management library. Implements fast transforms between ICC profiles. It is focused on speed, and is portable across several platforms (MIT license). | |
| lddist | ||
| lerc | Limited Error Raster Compression. | |
| libaec | Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). It implements Golomb-Rice compression method under the BSD license and includes a free drop-in replacement for the SZIP library. | |
| libaio | Linux native Asynchronous I/O interface library. | |
| libarchive | libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats. | |
| libatomic-ops | This package provides semi-portable access to hardware-provided atomic memory update operations on a number architectures. | |
| libav | ||
| libbeagle | Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. | |
| libbsd | This library provides useful functions commonly found on BSD systems, and lacking on others like GNU systems, thus making it easier to port projects with strong BSD origins, without needing to embed the same code over and over again on each project. | |
| libcerf | A self-contained C library providing complex error functions, based on Faddeevas plasma dispersion function w(z). Also provides Dawsons integral and Voigts convolution of a Gaussian and a Lorentzian | |
| libcifpp | ||
| libcroco | Libcroco is a standalone css2 parsing and manipulation library. | |
| libctl | ||
| libdeflate | Heavily optimized library for DEFLATE/zlib/gzip compression and decompression | |
| libdivsufsort | libdivsufsort is a software library that implements a lightweight suffix array construction algorithm. | |
| libdrm | A userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other systems supporting the ioctl interface. | |
| libedit | An autotools compatible port of the NetBSD editline library | |
| libelf | libelf lets you read, modify or create ELF object files in an architecture-independent way. The library takes care of size and endian issues, e.g. you can process a file for SPARC processors on an Intel-based system. Note: libelf is no longer maintained and packages that depend on libelf should migrate to elfutils. | |
| libepoxy | Epoxy is a library for handling OpenGL function pointer management for you. | |
| libevent | The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. | |
| libfabric | The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications. | |
| libffi | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time. | |
| libfontenc | libfontenc - font encoding library. | |
| libgcrypt | Cryptographic library based on the code from GnuPG. | |
| libgd | GD is an open source code library for the dynamic creation of images by programmers. GD is written in C, and wrappers are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM, BMP images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development. | |
| libgeotiff | GeoTIFF represents an effort by over 160 different remote sensing, GIS, cartographic, and surveying related companies and organizations to establish a TIFF based interchange format for georeferenced raster imagery. | |
| libgff | Lightweight GTF/GFF Parser, exposes a C++ interface without drawing in a heavyweight dependency. | |
| libgit2 | libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings. | |
| libgpg-error | Common error values for all GnuPG components. | |
| libice | libICE - Inter-Client Exchange Library. | |
| libiconv | GNU libiconv provides an implementation of the iconv() function and the iconv program for character set conversion. | |
| libidn2 | Libidn2 is a free software implementation of IDNA2008, Punycode and TR46. Its purpose is to encode and decode internationalized domain names. | |
| libimagequant | Small, portable C library for high-quality conversion of RGBA images to 8-bit indexed-color (palette) images. | |
| libint | Libint is a high-performance library for computing Gaussian integrals in quantum mechanics. | |
| libjpeg-turbo | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. | |
| libkml | Reference implementation of OGC KML 2.2. | |
| libmcfp | ||
| libmd | This library provides message digest functions found on BSD systems either on their libc (NetBSD, OpenBSD) or libmd (FreeBSD, DragonflyBSD, macOS, Solaris) libraries and lacking on others like GNU systems. | |
| libmng | THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image format. | |
| libnl | libnl - Netlink Protocol Library Suite | |
| libogg | Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. | |
| libpaper | The paper library and accompanying files are intended to provide a simple way for applications to take actions based on a system- or user-specified paper size. | |
| libpciaccess | Generic PCI access library. | |
| libpng | libpng is the official PNG reference library. | |
| libpsl | libpsl - C library to handle the Public Suffix List. | |
| libpthread-stubs | The libpthread-stubs package provides weak aliases for pthread functions not provided in libc or otherwise available by default. | |
| librsvg | Library to render SVG files using Cairo | |
| libsecret | libsecret is a library for storing and retrieving passwords and other secrets. It communicates with the Secret Service using D-Bus. gnome-keyring and ksecretservice are both implementations of a Secret Service. | |
| libsigsegv | GNU libsigsegv is a library for handling page faults in user mode. | |
| libsm | libSM - X Session Management Library. | |
| libsodium | Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. | |
| libsolv | Library for solving packages and reading repositories. | |
| libssh | libssh: the SSH library | |
| libssh2 | libssh2 is a client-side C library implementing the SSH2 protocol | |
| libszip | Szip is an implementation of the extended-Rice lossless compression algorithm. | |
| libtheora | Theora Video Compression. | |
| libtiff | LibTIFF - Tag Image File Format (TIFF) Library and Utilities. | |
| libtool | libtool — library building part of autotools. | |
| libunistring | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. | |
| libunwind | A portable and efficient C programming interface (API) to determine the call-chain of a program. | |
| libuuid | Portable uuid C library | |
| libvdwxc | Portable C library of density functionals with van der Waals interactions for density functional theory | |
| libvorbis | Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format for mid to high quality (8kHz- 48.0kHz, 16+ bit, polyphonic) audio and music at fixed and variable bitrates from 16 to 128 kbps/channel. | |
| libvori | Support for Voronoi Integration and lossless BQB compression | |
| libvpx | libvpx is a free software video codec library from Google and the Alliance for Open Media. It serves as the reference software implementation for the VP8 and VP9 video coding formats, and for AV1 a special fork named libaom that was stripped of backwards compatibility. | |
| libwebp | WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster. | |
| libx11 | libX11 - Core X11 protocol client library. | |
| libxau | The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. | |
| libxaw | Xaw is the X Athena Widget Set. Xaw is a widget set based on the X Toolkit Intrinsics (Xt) Library. | |
| libxc | Libxc is a library of exchange-correlation functionals for density-functional theory. | |
| libxcb | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. | |
| libxdamage | This package contains the library for the X Damage extension. | |
| libxdmcp | libXdmcp - X Display Manager Control Protocol library. | |
| libxext | libXext - library for common extensions to the X11 protocol. | |
| libxfixes | This package contains header files and documentation for the XFIXES extension. Library and server implementations are separate. | |
| libxfont | libXfont provides the core of the legacy X11 font system, handling the index files (fonts.dir, fonts.alias, fonts.scale), the various font file formats, and rasterizing them. It is used by the X servers, the X Font Server (xfs), and some font utilities (bdftopcf for instance), but should not be used by normal X11 clients. X11 clients access fonts via either the new APIs in libXft, or the legacy APIs in libX11. | |
| libxft | X FreeType library. | |
| libxi | libXi - library for the X Input Extension. | |
| libxinerama | libXinerama - API for Xinerama extension to X11 Protocol. | |
| libxkbcommon | xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. Its mainly meant for client toolkits, window systems, and other system applications. | |
| libxkbfile | XKB file handling routines. | |
| libxml2 | Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License. | |
| libxmu | This library contains miscellaneous utilities and is not part of the Xlib standard. It contains routines which only use public interfaces so that it may be layered on top of any proprietary implementation of Xlib or Xt. | |
| libxpm | libXpm - X Pixmap (XPM) image file format library. | |
| libxrandr | libXrandr - X Resize, Rotate and Reflection extension library. | |
| libxrender | libXrender - library for the Render Extension to the X11 protocol. | |
| libxscrnsaver | XScreenSaver - X11 Screen Saver extension client library | |
| libxslt | Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML. Libxslt is based on libxml2 the XML C library developed for the GNOME project. It also implements most of the EXSLT set of processor-portable extensions functions and some of Saxons evaluate and expressions extensions. | |
| libxsmm | Library targeting Intel Architecture for specialized dense and sparse matrix operations, and deep learning primitives. | |
| libxt | libXt - X Toolkit Intrinsics library. | |
| libxtst | libXtst provides the Xlib-based client API for the XTEST RECORD extensions. | |
| libxv | libXv - library for the X Video (Xv) extension to the X Window System. | |
| libxxf86vm | libXxf86vm - Extension library for the XFree86-VidMode X extension. | |
| libyaml | A C library for parsing and emitting YAML. | |
| libzip | libzip is a C library for reading, creating, and modifying zip archives. | |
| libzmq | The ZMQ networking/concurrency library and core API | |
| liggghts | Discrete element method particle simulation. | |
| lighttpd | a secure, fast, compliant and very flexible web-server | |
| links | ||
| llvm | The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries that can be used to build them. The name LLVM itself is not an acronym; it is the full name of the project. | |
| lmdb | Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. | |
| lndir | lndir - create a shadow directory of symbolic links to another directory tree. | |
| lobster | ||
| lobstr | ||
| log4cpp | log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily granular control over log management and configuration. | |
| longranger | ||
| lors | ||
| lp-solve | lp_solve is a Mixed Integer Linear Programming (MILP) solver. | |
| ltr_retriever | ||
| ltrdigest | ||
| lua-luafilesystem | LuaFileSystem is a Lua library developed to complement the set of functions related to file systems offered by the standard Lua distribution. | |
| lua-luaposix | Lua posix bindings, including ncurses | |
| lua-mpack | lua bindings to libmpack | |
| lua-sol2 | sol2 is a C++ library binding to Lua. | |
| lua | The Lua programming language interpreter and library. | |
| lz4 | LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalable with multi-cores CPU. It also features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems. | |
| lzo | Real-time data compression library |
M
| module name | link to docs | description |
|---|---|---|
| m4 | GNU M4 is an implementation of the traditional Unix macro processor. | |
| mafft | MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of ~200 sequences), FFT-NS-2 (fast; for alignment of ~30,000 sequences), etc. | |
| magics | Magics is the latest generation of the ECMWFs Meteorological plotting software MAGICS. Although completely redesigned in C++, it is intended to be as backwards-compatible as possible with the Fortran interface. | |
| makedepend | makedepend - create dependencies in makefiles. | |
| maker | ||
| malt | ||
| mambaforge | ||
| maple | maple | |
| mash | ||
| masurca | masurca | MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. |
| mathematica | ||
| matio | matio is an C library for reading and writing Matlab MAT files | |
| matlab | matlab | |
| maven | Apache Maven is a software project management and comprehension tool. | |
| maxbin | ||
| mbedtls | mbed TLS (formerly known as PolarSSL) makes it trivially easy for developers to include cryptographic and SSL/TLS capabilities in their (embedded) products, facilitating this functionality with a minimal coding footprint. | |
| mcl | The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. | |
| mcscanx | ||
| medaka | medaka | |
| meep | ||
| megahit | ||
| meme-suite | ||
| meme | meme | The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. |
| meraculous | ||
| mercurial | Mercurial is a free, distributed source control management tool. | |
| mesa-glu | This package provides the Mesa OpenGL Utility library. | |
| mesa | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. | |
| meson | Meson is a portable open source build system meant to be both extremely fast, and as user friendly as possible. | |
| meta | ||
| metabase | metabase | |
| metabat | MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. | |
| metashot | ||
| metis | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. | |
| micromamba | ||
| micropipe | ||
| migrate | migrate | |
| miniasm | ||
| minidot | ||
| minimap | ||
| minimap2 | Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Mappy provides a convenient interface to minimap2. | |
| minipolish | ||
| minizip | C library for zip/unzip via zLib. | |
| mira | ||
| mitobim | ||
| mkfontdir | mkfontdir creates the fonts.dir files needed by the legacy X server core font system. The current implementation is a simple wrapper script around the mkfontscale program, which must be built and installed first. | |
| mkfontscale | mkfontscale creates the fonts.scale and fonts.dir index files used by the legacy X11 font system. | |
| mkl | ||
| mlip2 | MLIP version 2. MLIP is a software for Machine Learning Interatomic Potentials. It has been developed at Skoltech (Moscow) by Alexander Shapeev, Evgeny Podryabinkin, Konstantin Gubaev, and Ivan Novikov | |
| mlip3 | MLIP version 3. MLIP is a software for Machine Learning Interatomic Potentials. It has been developed at Skoltech (Moscow) by Alexander Shapeev, Evgeny Podryabinkin, Konstantin Gubaev, and Ivan Novikov | |
| modeller | modeller | |
| modeltest | ||
| moe | ||
| molden | molden | A package for displaying Molecular Density from various Ab Initio packages |
| molpro | molpro | |
| mono | Mono is a software platform designed to allow developers to easily create cross platform applications. It is an open source implementation of Microsofts .NET Framework based on the ECMA standards for C and the Common Language Runtime. | |
| mopac | mopac | |
| mothur | mothur | This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. |
| mpc | Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. | |
| mpest | ||
| mpfr | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. | |
| mpich | ||
| mpich2 | ||
| mpich3 | ||
| mptp | ||
| mrbayes | mrbayes | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. |
| mrcc | ||
| mscgen | Mscgen is a small program that parses Message Sequence Chart descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as the output. | |
| msgpack-c | A small, fast binary interchange format convertible to/from JSON | |
| mstatx | ||
| mugsy | ||
| mummer | ||
| mumps | MUMPS: a MUltifrontal Massively Parallel sparse direct Solver | |
| muscle | MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. | |
| musket | ||
| mvapich | ||
| mysql | MySQL is an open source relational database management system. | |
| mysqlpp | MySQL++ is a C++ wrapper for MySQL and MariaDB C APIs. It is built on the same principles as the Standard C++ Library to make dealing with the database as easy as dealing with std containers. MySQL++ also provides facilities that let you avoid the most repetitive sorts of SQL within your own code, providing native C++ interfaces for these common tasks. | |
| mzmine3 |
N
| module name | link to docs | description |
|---|---|---|
| NAMD | ||
| namd | namd | NAMDis a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
| namd3.0_alpha9 | ||
| nanopolish | ||
| nanoporeworkflow | ||
| nasm | NASM (Netwide Assembler) is an 80x86 assembler designed for portability and modularity. It includes a disassembler as well. | |
| ncbi-magicblast | Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. | |
| ncbi-rmblastn | RMBlast search engine for NCBI | |
| nccl | Optimized primitives for collective multi-GPU communication. | |
| ncl | ||
| ncurses | The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD curses. | |
| ncview | Simple viewer for NetCDF files. | |
| necat | ||
| neighcrys | ||
| neper | ||
| netcdf-c | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the C distribution. | |
| netcdf-cxx | Deprecated C++ compatibility bindings for NetCDF. These do NOT read or write NetCDF-4 files, and are no longer maintained by Unidata. Developers should migrate to current NetCDF C++ bindings, in Spack package netcdf-cxx4. | |
| netcdf-fortran | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the Fortran distribution. | |
| netcdf | ||
| netlib-scalapack | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines | |
| netlib-xblas | XBLAS is a reference implementation for extra precision BLAS. | |
| nettle | The Nettle package contains the low-level cryptographic library that is designed to fit easily in many contexts. | |
| newick-utils | ||
| newton-x | ||
| nextflow | nextflow | |
| nextpolish | ||
| nfft | NFFT is a C subroutine library for computing the nonequispaced discrete Fourier transform (NDFT) in one or more dimensions, of arbitrary input size, and of complex data. | |
| nfs4acl | ||
| nghttp2 | nghttp2 is an implementation of HTTP/2 and its header compression algorithm HPACK in C. | |
| ngsparalog | ||
| ninja | Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible. | |
| nlohmann-json | JSON for Modern C++ | |
| nlopt | NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. | |
| node-js | Node.js is a JavaScript runtime built on Chromes V8 JavaScript engine. | |
| npm | npm @11.1.0 | |
| nrgljubljana | ||
| nrp-cmd | ||
| ntjoin | ||
| numactl | NUMA support for Linux | |
| numpy | ||
| nvhpc | The NVIDIA HPC SDK is a comprehensive suite of compilers, libraries and tools essential to maximizing developer productivity and the performance and portability of HPC applications. The NVIDIA HPC SDK C, C++, and Fortran compilers support GPU acceleration of HPC modeling and simulation applications with standard C++ and Fortran, OpenACC directives, and CUDA. GPU-accelerated math libraries maximize performance on common HPC algorithms, and optimized communications libraries enable standards-based multi-GPU and scalable systems programming. Performance profiling and debugging tools simplify porting and optimization of HPC applications. | |
| nwchem | High-performance computational chemistry software |
O
| module name | link to docs | description |
|---|---|---|
| oases | ||
| ocaml | OCaml is an industrial strength programming language supporting functional, imperative and object-oriented styles | |
| oclicd | ||
| ococo | ||
| octave | GNU Octave is a high-level language, primarily intended for numerical computations. | |
| octopus | A real-space finite-difference (time-dependent) density-functional theory code. | |
| ofed | ||
| omnic | ||
| onetools | ||
| opa-psm2 | Intel Omni-Path Performance Scaled Messaging 2 (PSM2) library | |
| openbabel | ||
| openblas | OpenBLAS: An optimized BLAS library | |
| opencv | opencv | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. |
| openfoam | openfoam | |
| openfst | ||
| openjdk | The free and opensource java implementation | |
| openjpeg | OpenJPEG is an open-source JPEG 2000 codec written in C language. | |
| openmolcas | OpenMolcas is a quantum chemistry software package. The key feature of OpenMolcas is the multiconfigurational approach to the electronic structure. | |
| openmpi | An open source Message Passing Interface implementation. | |
| openms | openms | |
| openmx | OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. | |
| opennebula-tools | ||
| openpbs | ||
| openssh | OpenSSH is the premier connectivity tool for remote login with the SSH protocol. It encrypts all traffic to eliminate eavesdropping, connection hijacking, and other attacks. In addition, OpenSSH provides a large suite of secure tunneling capabilities, several authentication methods, and sophisticated configuration options. | |
| openssl | OpenSSL is an open source project that provides a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library. | |
| operams | ||
| opus | Opus is a totally open, royalty-free, highly versatile audio codec. | |
| orc | the smallest, fastest columnar storage for Hadoop workloads. | |
| orca | orca | An ab initio, DFT and semiempirical SCF-MO package |
| orthofinder | OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. | |
| osi | Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming. | |
| osmesa | ||
| owncloud |
P
| module name | link to docs | description |
|---|---|---|
| p4vasp | ||
| packmol | Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. | |
| pairfq | ||
| palm | ||
| paml | PAML is a package of programs for phylogenetic analyses of DNA or protein sewuences using maximum likelihood. | |
| pandoc | If you need to convert files from one markup format into another, pandoc is your swiss-army knife. | |
| pango | Pango is a library for laying out and rendering of text, with an emphasis on internationalization. It can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. | |
| parallel-netcdf | PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for accessing files in format compatibility with Unidatas NetCDF, specifically the formats of CDF-1, 2, and 5. | |
| parallel | parallel | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. |
| paraview | ParaView is an open-source, multi-platform data analysis and visualization application. This package includes the Catalyst in-situ library for versions 5.7 and greater, otherwise use the catalyst package. | |
| pardre | ||
| parmetis | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. | |
| parmgridgen | MGRIDGEN is a serial library written entirely in ANSI C that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. ParMGridGen is the parallel version of MGridGen. | |
| partitionfinder | ||
| pasa | ||
| paup | paup | |
| pbbam | The pbbam software package provides components to create, query, edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities. | |
| pbdagcon | pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus). | |
| pbutgcns | DAG-based consensus caller for celera assemblers unitigs. It is currently tested only using pacbio corrected reads, though in prinicipal it could be used for pacbio un-corrected. It currently uses a simple python adapter to interface with the tigStore. Eventually, this is expected to be replaced with a more direct call to lower-level API calls. | |
| pcgamess | ||
| pcre | The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5. | |
| pcre2 | The PCRE2 package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5. | |
| pear | ||
| pegtl | The Parsing Expression Grammar Template Library (PEGTL) is a zero-dependency C++11 header-only library for creating parsers according to a Parsing Expression Grammar (PEG). | |
| perl-acme-damn | Acme::Damn provides a single routine, damn(), which takes a blessed reference (a Perl object), and unblesses it, to return the original reference. | |
| perl-algorithm-diff | Compute intelligent differences between two files / lists | |
| perl-alien-build | This module provides tools for building external (non-CPAN) dependencies for CPAN. It is mainly designed to be used at install time of a CPAN client, and work closely with Alien::Base which is used at runtime. | |
| perl-alien-libxml2 | This module provides libxml2 for other modules to use. | |
| perl-alien-svn | Perl SVN extension. | |
| perl-bioperl | BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documentation, but they also interact - Alignment objects are made from the Sequence objects, Sequence objects have access to Annotation and SeqFeature objects and databases, Blast objects can be converted to Alignment objects, and so on. This means that the objects provide a coordinated and extensible framework to do computational biology. | |
| perl-bit-vector | Efficient bit vector, set of integers and big int math library | |
| perl-capture-tiny | Capture STDOUT and STDERR from Perl, XS or external programs | |
| perl-carp-clan | Report errors from perspective of caller of a clan of modules | |
| perl-cgi | CGI - Handle Common Gateway Interface requests and responses | |
| perl-class-data-inheritable | For creating accessor/mutators to class data. | |
| perl-clone-choose | Checks several different modules which provides a clone() function and selects an appropriate one. | |
| perl-config-simple | Config::Simple - Simple Config Module | |
| perl-data-dumper | Stringified perl data structures, suitable for both printing and eval | |
| perl-data-stag | Structured Tags datastructures | |
| perl-db-file | DB_File is a module which allows Perl programs to make use of the facilities provided by Berkeley DB version 1.x (if you have a newer version of DB, see Using DB_File with Berkeley DB version 2 or greater). It is assumed that you have a copy of the Berkeley DB manual pages at hand when reading this documentation. The interface defined here mirrors the Berkeley DB interface closely. | |
| perl-dbd-mysql | MySQL driver for the Perl5 Database Interface (DBI) | |
| perl-dbd-pg | DBD::Pg is a Perl module that works with the DBI module to provide access to PostgreSQL databases. | |
| perl-dbd-sqlite | DBD::SQLite - Self-contained RDBMS in a DBI Driver | |
| perl-dbi | The DBI is the standard database interface module for Perl. It defines a set of methods, variables and conventions that provide a consistent database interface independent of the actual database being used. | |
| perl-devel-stacktrace | An object representing a stack trace. | |
| perl-devel-symdump | Devel::Symdump - dump symbol names or the symbol table | |
| perl-encode-locale | Determine the locale encoding | |
| perl-error | The Error package provides two interfaces. Firstly Error provides a procedural interface to exception handling. Secondly Error is a base class for errors/exceptions that can either be thrown, for subsequent catch, or can simply be recorded. | |
| perl-exception-class | A module that allows you to declare real exception classes in Perl | |
| perl-exporter-tiny | An exporter with the features of Sub::Exporter but only core dependencies | |
| perl-extutils-config | ExtUtils::Config - A wrapper for perls configuration | |
| perl-extutils-helpers | ExtUtils::Helpers - Various portability utilities for module builders | |
| perl-extutils-installpaths | ExtUtils::InstallPaths - Build.PL install path logic made easy | |
| perl-extutils-makemaker | ExtUtils::MakeMaker - Create a module Makefile. This utility is designed to write a Makefile for an extension module from a Makefile.PL. It is based on the Makefile.SH model provided by Andy Dougherty and the perl5-porters. | |
| perl-extutils-pkgconfig | simplistic interface to pkg-config | |
| perl-ffi-checklib | This module checks whether a particular dynamic library is available for FFI to use. It is modeled heavily on Devel::CheckLib, but will find dynamic libraries even when development packages are not installed. It also provides a find_lib function that will return the full path to the found dynamic library, which can be feed directly into FFI::Platypus or another FFI system. | |
| perl-file-chdir | Perls chdir() has the unfortunate problem of being very, very, very global. If any part of your program calls chdir() or if any library you use calls chdir(), it changes the current working directory for the whole program. | |
| perl-file-copy-recursive | Perl extension for recursively copying files and directories | |
| perl-file-homedir | Find your home and other directories on any platform | |
| perl-file-listing | Parse directory listing | |
| perl-file-sharedir-install | Install shared files | |
| perl-file-slurp-tiny | A simple, sane and efficient file slurper | |
| perl-file-which | Perl implementation of the which utility as an API | |
| perl-forks | The forks pragma allows a developer to use threads without having to have a threaded perl, or to even run 5.8.0 or higher. | |
| perl-gd-svg | SVG Graphics Module for Perl 5 | |
| perl-gd | Interface to Gd Graphics Library | |
| perl-gdgraph-histogram | GD::Graph::histogram extends the GD::Graph module to create histograms. The module allow creation of count or percentage histograms. | |
| perl-gdgraph | Graph Plotting Module for Perl 5 | |
| perl-gdtextutil | Text utilities for use with GD | |
| perl-graph | Graph data structures and algorithms | |
| perl-hash-merge | Hash::Merge merges two arbitrarily deep hashes into a single hash. | |
| perl-html-parser | HTML parser class | |
| perl-html-tagset | Data tables useful in parsing HTML | |
| perl-http-cookies | HTTP cookie jars | |
| perl-http-daemon | A simple http server class | |
| perl-http-date | Date conversion routines | |
| perl-http-message | HTTP style message (base class) | |
| perl-http-negotiate | Choose a variant to serve | |
| perl-inline-c | C Language Support for Inline | |
| perl-inline | Write Perl Subroutines in Other Programming Languages | |
| perl-io-all | IO::All combines all of the best Perl IO modules into a single nifty object oriented interface to greatly simplify your everyday Perl IO idioms. It exports a single function called io, which returns a new IO::All object. And that object can do it all! | |
| perl-io-html | Open an HTML file with automatic charset detection. | |
| perl-io-prompt | By default, this module exports a single function prompt. It prompts the user to enter some input, and returns an object that represents the user input. | |
| perl-io-socket-ssl | SSL sockets with IO::Socket interface | |
| perl-io-string | Emulate file interface for in-core strings | |
| perl-io-stringy | This toolkit primarily provides modules for performing both traditional and object-oriented i/o) on things other than normal filehandles; in particular, IO::Scalar, IO::ScalarArray, and IO::Lines. | |
| perl-io-tty | IO::Tty is used internally by IO::Pty to create a pseudo-tty. You wouldnt want to use it directly except to import constants, use IO::Pty. For a list of importable constants, see IO::Tty::Constant. | |
| perl-ipc-run | IPC::Run allows you to run and interact with child processes using files, pipes, and pseudo-ttys. Both system()-style and scripted usages are supported and may be mixed. Likewise, functional and OO API styles are both supported and may be mixed. | |
| perl-libwww-perl | The libwww-perl collection is a set of Perl modules which provides a simple and consistent application programming interface to the World-Wide Web. The main focus of the library is to provide classes and functions that allow you to write WWW clients. | |
| perl-libxml-perl | libxml-perl is a collection of smaller Perl modules, scripts, and documents for working with XML in Perl. libxml-perl software works in combination with XML::Parser, PerlSAX, XML::DOM, XML::Grove and others. | |
| perl-list-moreutils-xs | List::MoreUtils::XS is a backend for List::MoreUtils. Even if its possible (because of user wishes) to have it practically independent from List::MoreUtils, it technically depend on List::MoreUtils. Since its only a backend, the API is not public and can change without any warning. | |
| perl-list-moreutils | Provide the stuff missing in List::Util | |
| perl-logger-simple | Implementation of the Simran-Log-Log and Simran-Error-Error modules | |
| perl-lwp-mediatypes | Guess media type for a file or a URL | |
| perl-lwp-protocol-https | Provide https support for LWP::UserAgent | |
| perl-mailtools | Perl module for handling mail | |
| perl-math-utils | Math::Utils - Perl extension | |
| perl-mce | MCE - Many-Core Engine for Perl providing parallel processing capabilities. | |
| perl-module-build-tiny | Module::Build::Tiny - A tiny replacement for Module::Build | |
| perl-module-build | Module::Build is a system for building, testing, and installing Perl modules. It is meant to be an alternative to ExtUtils::MakeMaker. Developers may alter the behavior of the module through subclassing in a much more straightforward way than with MakeMaker. It also does not require a make on your system - most of the Module::Build code is pure-perl and written in a very cross-platform way. | |
| perl-mozilla-ca | Mozillas CA cert bundle in PEM format | |
| perl-net-http | Low-level HTTP connection (client) | |
| perl-net-ssleay | Perl extension for using OpenSSL | |
| perl-object-insideout | Implements inside-out objects as anonymous scalar references that are blessed into a class with the scalar containing the ID for the object (usually a sequence number). | |
| perl-parallel-forkmanager | A simple parallel processing fork manager | |
| perl-parse-recdescent | Generate Recursive-Descent Parsers | |
| perl-path-tiny | This module provides a small, fast utility for working with file paths. It is friendlier to use than File::Spec and provides easy access to functions from several other core file handling modules. It aims to be smaller and faster than many alternatives on CPAN, while helping people do many common things in consistent and less error-prone ways. | |
| perl-pegex | Acmeist PEG Parser Framework | |
| perl-perl-unsafe-signals | Quoting perl581delta: | |
| perl-readonly | Readonly - Facility for creating read-only scalars, arrays, hashes | |
| perl-scalar-list-utils | Scalar::Util - A selection of general-utility scalar subroutines | |
| perl-scalar-util-numeric | This module exports a number of wrappers around perls builtin grok_number function, which returns the numeric type of its argument, or 0 if it isnt numeric. | |
| perl-set-scalar | Set::Scalar - basic set operations | |
| perl-sub-uplevel | apparently run a function in a higher stack frame | |
| perl-svg | Perl extension for generating Scalable Vector Graphics (SVG) documents. | |
| perl-sys-sigaction | Prior to version 5.8.0 perl implemented unsafe signal handling. The reason it is consider unsafe, is that there is a risk that a signal will arrive, and be handled while perl is changing internal data structures. This can result in all kinds of subtle and not so subtle problems. For this reason it has always been recommended that one do as little as possible in a signal handler, and only variables that already exist be manipulated. | |
| perl-term-ansicolor | Color screen output using ANSI escape sequences | |
| perl-termreadkey | Term::ReadKey is a compiled perl module dedicated to providing simple control over terminal driver modes (cbreak, raw, cooked, etc.,) support for non-blocking reads, if the architecture allows, and some generalized handy functions for working with terminals. One of the main goals is to have the functions as portable as possible, so you can just plug in use Term::ReadKey on any architecture and have a good likelihood of it working. | |
| perl-test-deep | Extremely flexible deep comparison | |
| perl-test-differences | Test strings and data structures and show differences if not ok | |
| perl-test-exception | Test exception-based code | |
| perl-test-most | Most commonly needed test functions and features. | |
| perl-test-needs | Skip tests when modules not available. | |
| perl-test-requiresinternet | Easily test network connectivity | |
| perl-test-warn | Perl extension to test methods for warnings | |
| perl-text-diff | Provides a basic set of services akin to the GNU diff utility. | |
| perl-text-soundex | Soundex is a phonetic algorithm for indexing names by sound, as pronounced in English. The goal is for names with the same pronunciation to be encoded to the same representation so that they can be matched despite minor differences in spelling | |
| perl-thread-queue | Thread::Queue - Thread-safe queues. | |
| perl-threads | threads - Perl interpreter-based threads | |
| perl-timedate | The parser contained here will only parse absolute dates, if you want a date parser that can parse relative dates then take a look at the Time modules by David Muir on CPAN. | |
| perl-tk | Interface to Tk Graphics Library | |
| perl-try-tiny | Minimal try/catch with proper preservation of $@ | |
| perl-uri | Uniform Resource Identifiers (absolute and relative) | |
| perl-want | A generalisation of wantarray. | |
| perl-www-robotrules | Database of robots.txt-derived permissions | |
| perl-xml-dom-xpath | XML::DOM::XPath allows you to use XML::XPath methods to query a DOM. This is often much easier than relying only on getElementsByTagName. | |
| perl-xml-dom | This module extends the XML::Parser module by Clark Cooper. The XML::Parser module is built on top of XML::Parser::Expat, which is a lower level interface to James Clarks expat library. | |
| perl-xml-filter-buffertext | This is a very simple filter. One common cause of grief (and programmer error) is that XML parsers arent required to provide character events in one chunk. They can, but are not forced to, and most dont. This filter does the trivial but oft-repeated task of putting all characters into a single event. | |
| perl-xml-libxml | This module is an interface to libxml2, providing XML and HTML parsers with DOM, SAX and XMLReader interfaces, a large subset of DOM Layer 3 interface and a XML::XPath-like interface to XPath API of libxml2. The module is split into several packages which are not described in this section; unless stated otherwise, you only need to use XML::LibXML; in your programs. | |
| perl-xml-namespacesupport | This module offers a simple to process namespaced XML names (unames) from within any application that may need them. It also helps maintain a prefix to namespace URI map, and provides a number of basic checks. | |
| perl-xml-parser | XML::Parser - A perl module for parsing XML documents | |
| perl-xml-quote | This module provides functions to quote/dequote strings in xml-way. | |
| perl-xml-regexp | This package contains regular expressions for the following XML tokens: BaseChar, Ideographic, Letter, Digit, Extender, CombiningChar, NameChar, EntityRef, CharRef, Reference, Name, NmToken, and AttValue. | |
| perl-xml-sax-base | This module has a very simple task - to be a base class for PerlSAX drivers and filters. Its default behaviour is to pass the input directly to the output unchanged. It can be useful to use this module as a base class so you dont have to, for example, implement the characters() callback. | |
| perl-xml-sax-writer | A new XML Writer was needed to match the SAX2 effort because quite naturally no existing writer understood SAX2. My first intention had been to start patching XML::Handler::YAWriter as it had previously been my favourite writer in the SAX1 world. | |
| perl-xml-sax | XML::SAX is a SAX parser access API for Perl. It includes classes and APIs required for implementing SAX drivers, along with a factory class for returning any SAX parser installed on the users system. | |
| perl-xml-simple | An API for simple XML files | |
| perl-xml-twig | This module provides a way to process XML documents. It is build on top of XML::Parser. | |
| perl-xml-writer | XML::Writer is a helper module for Perl programs that write an XML document. The module handles all escaping for attribute values and character data and constructs different types of markup, such as tags, comments, and processing instructions. | |
| perl-xml-xpathengine | This module provides an XPath engine, that can be re-used by other module/classes that implement trees. | |
| perl-yaml-libyaml | Perl YAML Serialization using XS and libyaml | |
| perl-yaml | This module has been released to CPAN as YAML::Old, and soon YAML.pm will be changed to just be a frontend interface module for all the various Perl YAML implementation modules, including YAML::Old | |
| perl | Perl 5 is a highly capable, feature-rich programming language with over 27 years of development. | |
| perun | ||
| pexsi | The PEXSI library is written in C++, and uses message passing interface (MPI) to parallelize the computation on distributed memory computing systems and achieve scalability on more than 10,000 processors. | |
| pfft | PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition. | |
| pgicdk | ||
| pgiwks | ||
| phonopy | ||
| php | ||
| phylip | ||
| phylobayes | ||
| phylobayesmpi | Phylobayes MPI version | |
| phylomagnet | ||
| phyml | ||
| phyparts | ||
| phyx | ||
| picard | picard | |
| pilon | Pilon is an automated genome assembly improvement and variant detection tool. | |
| pinfo | Pinfo is user-friendly, console-based viewer for Info documents. | |
| piranha | ||
| pixman | The Pixman package contains a library that provides low-level pixel manipulation features such as image compositing and trapezoid rasterization. | |
| pkgconf | pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility. | |
| platanus | platanus | |
| platon | ||
| plink | ||
| plumed | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. | |
| pmin | ||
| pmix | The Process Management Interface (PMI) has been used for quite some time as a means of exchanging wireup information needed for interprocess communication. However, meeting the significant orchestration challenges presented by exascale systems requires that the process-to-system interface evolve to permit a tighter integration between the different components of the parallel application and existing and future SMS solutions. | |
| poppler-data | This package consists of encoding files for use with poppler. The encoding files are optional and poppler will automatically read them if they are present. When installed, the encoding files enables poppler to correctly render CJK and Cyrrilic properly. While poppler is licensed under the GPL, these encoding files have different license, and thus distributed separately. | |
| poppler | Poppler is a PDF rendering library based on the xpdf-3.0 code base. | |
| porechop | ||
| portcullis | ||
| postgresql | PostgreSQL is a powerful, open source object-relational database system. It has more than 15 years of active development and a proven architecture that has earned it a strong reputation for reliability, data integrity, and correctness. | |
| povray | ||
| prank | ||
| preseq | ||
| prodigal | ||
| proj | PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations. | |
| protobuf | Googles data interchange format. | |
| psm | Intel Performance scaled messaging library | |
| pugixml | Light-weight, simple, and fast XML parser for C++ with XPath support | |
| purge-dups | ||
| py-absl-py | This repository is a collection of Python library code for building Python applications. | |
| py-alabaster | Alabaster is a visually (c)lean, responsive, configurable theme for the Sphinx documentation system. | |
| py-anyio | High level compatibility layer for multiple asynchronous event loop implementations. | |
| py-appdirs | A small Python module for determining appropriate platform-specific dirs, e.g. a user data dir. | |
| py-argon2-cffi-bindings | Low-level CFFI bindings for Argon2. | |
| py-argon2-cffi | The secure Argon2 password hashing algorithm.. | |
| py-ase | The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. | |
| py-asn1crypto | Python ASN.1 library with a focus on performance and a pythonic API | |
| py-astor | astor is designed to allow easy manipulation of Python source via the AST. | |
| py-asttokens | Annotate AST trees with source code positions. | |
| py-astunparse | An AST unparser for Python. | |
| py-attrs | Classes Without Boilerplate | |
| py-automat | Self-service finite-state machines for the programmer on the go. | |
| py-azure-common | Microsoft Azure Client Library for Python (Common). | |
| py-azure-core | Microsoft Azure Core Library for Python. | |
| py-azure-storage-blob | Microsoft Azure Blob Storage Client Library for Python | |
| py-babel | Babel is an integrated collection of utilities that assist in internationalizing and localizing Python applications, with an emphasis on web-based applications. | |
| py-backcall | Specifications for callback functions passed in to an API | |
| py-backports-entry-points-selectable | Compatibility shim providing selectable entry points for older implementations | |
| py-beautifulsoup4 | Beautiful Soup is a Python library for pulling data out of HTML and XML files. It works with your favorite parser to provide idiomatic ways of navigating, searching, and modifying the parse tree. | |
| py-beniget | Extract semantic information about static Python code. | |
| py-biopandas | Working with molecular structures in pandas DataFrames | |
| py-biopython | A distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. | |
| py-bitarray | Efficient array of booleans - C extension | |
| py-black | Black is the uncompromising Python code formatter. By using it, you agree to cede control over minutiae of hand-formatting. In return, Black gives you speed, determinism, and freedom from pycodestyle nagging about formatting. | |
| py-bleach | An easy whitelist-based HTML-sanitizing tool. | |
| py-blinker | Fast, simple object-to-object and broadcast signaling | |
| py-boto3 | The AWS SDK for Python. | |
| py-botocore | Low-level, data-driven core of boto 3. | |
| py-bottleneck | A collection of fast NumPy array functions written in Cython. | |
| py-brotlipy | Python binding to the Brotli library. | |
| py-bx-python | The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. | |
| py-bz2file | Python library for reading and writing bzip2-compressed files. | |
| py-cached-property | A decorator for caching properties in classes. | |
| py-cachetools | This module provides various memoizing collections and decorators, including variants of the Python 3 Standard Library @lru_cache function decorator. | |
| py-cairocffi | cairocffi is a CFFI-based drop-in replacement for Pycairo, a set of Python bindings and object-oriented API for cairo. Cairo is a 2D vector graphics library with support for multiple backends including image buffers, PNG, PostScript, PDF, and SVG file output. | |
| py-certifi | Certifi: A carefully curated collection of Root Certificates for validating the trustworthiness of SSL certificates while verifying the identity of TLS hosts. | |
| py-cffi | Foreign Function Interface for Python calling C code | |
| py-chardet | Universal encoding detector for Python 2 and 3 | |
| py-charset-normalizer | The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet. | |
| py-click | A simple wrapper around optparse for powerful command line utilities. | |
| py-cloudpickle | Extended pickling support for Python objects. | |
| py-colorama | Cross-platform colored terminal text. | |
| py-colormath | Color math and conversion library. | |
| py-configargparse | Applications with more than a handful of user-settable options are best configured through a combination of command line args, config files, hard-coded defaults, and in some cases, environment variables. | |
| py-connectionpool | Thread-safe connection pool for python. | |
| py-constantly | Symbolic constants in Python | |
| py-cppy | C++ headers for C extension development | |
| py-cryptography | cryptography is a package which provides cryptographic recipes and primitives to Python developers | |
| py-cssselect | Python-cssselect parses CSS3 Selectors and translate them to XPath 1.0 expressions. Such expressions can be used in lxml or another XPath engine to find the matching elements in an XML or HTML document. | |
| py-cutadapt | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. | |
| py-cycler | Composable style cycles. | |
| py-cython | The Cython compiler for writing C extensions for the Python language. | |
| py-dask | Dask is a flexible parallel computing library for analytics. | |
| py-datrie | Super-fast, efficiently stored Trie for Python (2.x and 3.x). Uses libdatrie. | |
| py-debugpy | An implementation of the Debug Adapter Protocol for Python. | |
| py-decorator | The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples. | |
| py-deeptools | deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. | |
| py-deeptoolsintervals | A python module creating/accessing GTF-based interval trees with associated meta-data. | |
| py-defusedxml | defusing XML bombs and other exploits | |
| py-deprecation | The deprecation library provides a deprecated decorator and a fail_if_not_removed decorator for your tests. | |
| py-distlib | Distribution utilities | |
| py-distributed | Distributed scheduler for Dask | |
| py-dnaio | Read and write FASTQ and FASTA | |
| py-docutils | Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language. | |
| py-entrypoints | Discover and load entry points from installed packages. | |
| py-espresso | ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, polyelectrolytes, ferrofluids and biological systems, for example DNA and lipid membranes. It also has a DPD and lattice Boltzmann solver for hydrodynamic interactions, and allows several particle couplings to the LB fluid. | |
| py-executing | Get the currently executing AST node of a frame, and other information. | |
| py-faststructure | FastStructure is a fast algorithm for inferring population structure from large SNP genotype data. | |
| py-ffq | ffq receives an accession and returns the metadata for that accession as well as the metadata for all downstream accessions following the connections between GEO, SRA, EMBL-EBI, DDBJ, and Biosample | |
| py-filelock | A platform-independent file lock for Python. | |
| py-flatbuffers | The FlatBuffers serialization format implemented in Python. For a faster and feature-complete version check out the C++ implementation in flatbuffers package. | |
| py-flit-core | Distribution-building parts of Flit. | |
| py-flit | Flit is a simple way to put Python packages and modules on PyPI. | |
| py-fonttools | fontTools is a library for manipulating fonts, written in Python. | |
| py-frozendict | frozendict is a simple immutable dictionary. Its fast as dict, and sometimes faster! | |
| py-fsspec | A specification for pythonic filesystems. | |
| py-future | Clean single-source support for Python 3 and 2 | |
| py-gast | Python AST that abstracts the underlying Python version | |
| py-gevent | gevent is a coroutine-based Python networking library. | |
| py-gitdb | The GitDB project implements interfaces to allow read and write access to git repositories. | |
| py-gitpython | GitPython is a python library used to interact with Git repositories. | |
| py-google-api-core | Google API client core library. | |
| py-google-api-python-client | The Google API Client for Python is a client library for accessing the Plus, Moderator, and many other Google APIs. | |
| py-google-auth-httplib2 | Google Authentication Library: httplib2 transport. | |
| py-google-auth-oauthlib | This library provides oauthlib integration with google-auth. | |
| py-google-auth | This library simplifies using Googles various server-to-server authentication mechanisms to access Google APIs. | |
| py-google-cloud-core | Google Cloud API client core library. | |
| py-google-cloud-storage | Google Cloud Storage API client library. | |
| py-google-crc32c | This package wraps the google/crc32c hardware-based implementation of the CRC32C hashing algorithm. | |
| py-google-pasta | pasta is an AST-based Python refactoring library. | |
| py-google-resumable-media | Utilities for Google Media Downloads and Resumable Uploads. | |
| py-googleapis-common-protos | Common protobufs used in Google APIs. | |
| py-gpaw | GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). | |
| py-greenlet | Lightweight in-process concurrent programming | |
| py-grpcio | HTTP/2-based RPC framework. | |
| py-h5py | The h5py package provides both a high- and low-level interface to the HDF5 library from Python. | |
| py-hapflk | ||
| py-heapdict | A heap with decrease-key and increase-key operations | |
| py-html5lib | HTML parser based on the WHATWG HTML specification. | |
| py-htseq | HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. | |
| py-httplib2 | A comprehensive HTTP client library. | |
| py-hyperlink | A featureful, immutable, and correct URL for Python. | |
| py-idna | Internationalized Domain Names for Python (IDNA 2008 and UTS 46) | |
| py-imageio | Python library for reading and writing image data. | |
| py-imagesize | Parses image file headers and returns image size. Supports PNG, JPEG, JPEG2000, and GIF image file formats. | |
| py-importlib-metadata | Read metadata from Python packages. | |
| py-incremental | A small library that versions your Python projects. | |
| py-ipykernel | IPython Kernel for Jupyter | |
| py-ipython-genutils | Vestigial utilities from IPython | |
| py-ipython | IPython provides a rich toolkit to help you make the most out of using Python interactively. | |
| py-ipywidgets | IPython widgets for the Jupyter Notebook | |
| py-isodate | This module implements ISO 8601 date, time and duration parsing. The implementation follows ISO8601:2004 standard, and implements only date/time representations mentioned in the standard. If something is not mentioned there, then it is treated as non existent, and not as an allowed option. | |
| py-jedi | An autocompletion tool for Python that can be used for text editors. | |
| py-jinja2 | Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment. | |
| py-jmespath | JSON Matching Expressions. | |
| py-joblib | Lightweight pipelining with Python functions. | |
| py-json5 | The JSON5 Data Interchange Format (JSON5) is a superset of JSON that aims to alleviate some of the limitations of JSON by expanding its syntax to include some productions from ECMAScript 5.1. | |
| py-jsonschema | Jsonschema: An(other) implementation of JSON Schema for Python. | |
| py-jupyter-client | Jupyter protocol client APIs | |
| py-jupyter-console | Jupyter Terminal Console | |
| py-jupyter-core | Core Jupyter functionality | |
| py-jupyter-packaging7 | Jupyter Packaging Utilities, version 7. | |
| py-jupyter-packaging11 | Jupyter Packaging Utilities, version 11. | |
| py-jupyter-server | The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila. | |
| py-jupyter | Jupyter metapackage. Install all the Jupyter components in one go. | |
| py-jupyterlab-pygments | Pygments theme using JupyterLab CSS variables. | |
| py-jupyterlab-server | A set of server components for JupyterLab and JupyterLab like applications | |
| py-jupyterlab-widgets | A JupyterLab extension. | |
| py-jupyterlab | JupyterLab is the next-generation web-based user interface for Project Jupyter. | |
| py-keras-applications | Sample Deep Learning application in Keras. Keras depends on this package to run properly. | |
| py-keras-preprocessing | Utilities for working with image data, text data, and sequence data. | |
| py-kerberos | This Python package is a high-level wrapper for Kerberos (GSSAPI) operations. The goal is to avoid having to build a module that wraps the entire Kerberos.framework, and instead offer a limited set of functions that do what is needed for client/server Kerberos authentication based on https://www.ietf.org/rfc/rfc4559.txt. | |
| py-khmer | k-mer counting, filtering, and graph traversal | |
| py-kiwisolver | A fast implementation of the Cassowary constraint solver | |
| py-libclang | The repository contains code that taken from the LLVM project, to make it easier to install clangs python bindings. | |
| py-lime | Local Interpretable Model-Agnostic Explanations for machine learning classifiers | |
| py-locket | File-based locks for Python for Linux and Windows. | |
| py-lxml | lxml is the most feature-rich and easy-to-use library for processing XML and HTML in the Python language. | |
| py-lzstring | lz-string for python. | |
| py-m2r | M2R converts a markdown file including reStructuredText (rst) markups to a valid rst format. | |
| py-mako | A super-fast templating language that borrows the best ideas from the existing templating languages. | |
| py-markdown | This is a Python implementation of John Grubers Markdown. It is almost completely compliant with the reference implementation, though there are a few very minor differences. See Johns Syntax Documentation for the syntax rules. | |
| py-markupsafe | MarkupSafe is a library for Python that implements a unicode string that is aware of HTML escaping rules and can be used to implement automatic string escaping. It is used by Jinja 2, the Mako templating engine, the Pylons web framework and many more. | |
| py-matplotlib-inline | Inline Matplotlib backend for Jupyter. | |
| py-matplotlib-venn | Routines for plotting area-weighted two- and three-circle venn diagrams. | |
| py-matplotlib | Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. | |
| py-mistune | A sane Markdown parser with useful plugins and renderers. | |
| py-more-itertools | Additions to the standard Python itertools package. | |
| py-mpi4py | This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings. | |
| py-msgpack | MessagePack (de)serializer. | |
| py-msrest | AutoRest swagger generator Python client runtime. | |
| py-multiqc | MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It is written in Python and contains modules for a large number of common bioinformatics tools. | |
| py-mypy-extensions | Experimental type system extensions for programs checked with the mypy typechecker. | |
| py-nbclassic | Jupyter Notebook as a Jupyter Server Extension. | |
| py-nbclient | A client library for executing notebooks. | |
| py-nbconvert | Jupyter Notebook Conversion | |
| py-nbformat | The Jupyter Notebook format | |
| py-nest-asyncio | Patch asyncio to allow nested event loops. | |
| py-networkx | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | |
| py-nose | nose extends the test loading and running features of unittest, making it easier to write, find and run tests. | |
| py-notebook | Jupyter Interactive Notebook | |
| py-numexpr | Fast numerical expression evaluator for NumPy | |
| py-numpy | NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities | |
| py-numpydoc | numpydoc - Numpys Sphinx extensions | |
| py-oauth2client | OAuth 2.0 client library. | |
| py-oauthlib | A generic, spec-compliant, thorough implementation of the OAuth request-signing logic | |
| py-opt-einsum | Optimized Einsum: A tensor contraction order optimizer. | |
| py-p4phylogenetics | P4 does Bayesian and maximum likelihood phylogenetic analyses on molecular sequences. Its specialty is that you can use heterogeneous models, where the model parameters can differ in different parts of the tree, or over different parts of the data. | |
| py-packaging | Core utilities for Python packages. | |
| py-pandas | pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language. | |
| py-pandocfilters | A python module for writing pandoc filters | |
| py-parabam | Extensions to the Python standard library unit testing framework. | |
| py-parso | Parso is a Python parser that supports error recovery and round-trip parsing for different Python versions (in multiple Python versions). Parso is also able to list multiple syntax errors in your python file. | |
| py-partd | Key-value byte store with appendable values. | |
| py-pathlib2 | Backport of pathlib from python 3.4 | |
| py-pathspec | pathspec extends the test loading and running features of unittest, making it easier to write, find and run tests. | |
| py-patsy | A Python package for describing statistical models and for building design matrices. | |
| py-pexpect | Pexpect allows easy control of interactive console applications. | |
| py-phonopy | Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels. | |
| py-pickleshare | Tiny shelve-like database with concurrency support | |
| py-pillow | Pillow is a fork of the Python Imaging Library (PIL). It adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. | |
| py-pip | The PyPA recommended tool for installing Python packages. | |
| py-pkgconfig | Interface Python with pkg-config. | |
| py-platformdirs | A small Python module for determining appropriate platform-specific dirs, e.g. a user data dir | |
| py-plotly | An interactive, browser-based graphing library for Python | |
| py-ply | Python Lex Yacc. | |
| py-poetry-core | Poetry PEP 517 Build Backend. | |
| py-prometheus-client | Prometheus instrumentation library for Python applications. | |
| py-prompt-toolkit | Library for building powerful interactive command lines in Python | |
| py-protobuf | Protocol buffers are Googles language-neutral, platform-neutral, extensible mechanism for serializing structured data - think XML, but smaller, faster, and simpler. You define how you want your data to be structured once, then you can use special generated source code to easily write and read your structured data to and from a variety of data streams and using a variety of languages. | |
| py-psutil | psutil is a cross-platform library for retrieving information on running processes and system utilization (CPU, memory, disks, network) in Python. | |
| py-ptyprocess | Run a subprocess in a pseudo terminal | |
| py-pulp | PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems. | |
| py-pure-eval | Safely evaluate AST nodes without side effects. | |
| py-pure-sasl | This package provides a reasonably high-level SASL client written in pure Python. New mechanisms may be integrated easily, but by default, support for PLAIN, ANONYMOUS, EXTERNAL, CRAM-MD5, DIGEST-MD5, and GSSAPI are provided. | |
| py-py | Library with cross-python path, ini-parsing, io, code, log facilities | |
| py-py2bit | A package for accessing 2bit files using lib2bit. | |
| py-pyarrow | A cross-language development platform for in-memory data. | |
| py-pyasn1-modules | A collection of ASN.1 modules expressed in form of pyasn1 classes. Includes protocols PDUs definition (SNMP, LDAP etc.) and various data structures (X.509, PKCS etc.). | |
| py-pyasn1 | Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208). | |
| py-pybedtools | Python wrapper — and more — for Aaron Quinlans BEDTools | |
| py-pybigwig | A package for accessing bigWig files using libBigWig. | |
| py-pybind11 | pybind11 — Seamless operability between C++11 and Python. | |
| py-pycairo | Pycairo is a set of Python bindings for the cairo graphics library. | |
| py-pycparser | A complete parser of the C language, written in pure python. | |
| py-pydoe2 | pyDOE2 is a fork of the pyDOE package that is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs. | |
| py-pyfasta | Pyfasta: fast, memory-efficient, pythonic (and command-line) access to fasta sequence files | |
| py-pygments | Pygments is a syntax highlighting package written in Python. | |
| py-pygobject | bindings for the GLib, and GObject, to be used in Python. | |
| py-pygraphviz | Python interface to Graphviz | |
| py-pyjwt | JSON Web Token implementation in Python | |
| py-pyopenssl | High-level wrapper around a subset of the OpenSSL library. | |
| py-pyparsing | A Python Parsing Module. | |
| py-pyqt5 | PyQt is a set of Python v2 and v3 bindings for The Qt Companys Qt application framework and runs on all platforms supported by Qt including Windows, OS X, Linux, iOS and Android. PyQt5 supports Qt v5. | |
| py-pyrad | RADseq for phylogenetics introgression analyses | |
| py-pyrsistent | Pyrsistent is a number of persistent collections (by some referred to as functional data structures). Persistent in the sense that they are immutable. | |
| py-pysam | A python module for reading, manipulating and writing genomic data sets. | |
| py-pysocks | A Python SOCKS client module. | |
| py-pytest-runner | Invoke py.test as distutils command with dependency resolution. | |
| py-python-dateutil | Extensions to the standard Python datetime module. | |
| py-python-levenshtein | Python extension for computing string edit distances and similarities. | |
| py-python-magic | A python wrapper for libmagic. | |
| py-pythran | Ahead of Time compiler for numeric kernels. | |
| py-pytz | World timezone definitions, modern and historical. | |
| py-pywavelets | PyWavelets is a free Open Source library for wavelet transforms in Python | |
| py-pyyaml | PyYAML is a YAML parser and emitter for Python. | |
| py-pyzmq | PyZMQ: Python bindings for zeromq. | |
| py-qtconsole | Jupyter Qt console | |
| py-qtpy | QtPy: Abtraction layer for PyQt5/PyQt4/PySide/PySide2 | |
| py-ratelimiter | Simple Python module providing rate limiting. | |
| py-reportlab | The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics. | |
| py-requests-oauthlib | This project provides first-class OAuth library support for Requests. | |
| py-requests | Python HTTP for Humans. | |
| py-rsa | Pure-Python RSA implementation | |
| py-rseqc | RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. | |
| py-rst2pdf | Convert reStructured Text to PDF via ReportLab. | |
| py-s3cmd | S3cmd (s3cmd) is a free command line tool and client for uploading, retrieving and managing data in Amazon S3 and other cloud storage service providers that use the S3 protocol, such as Google Cloud Storage or DreamHost DreamObjects. It is best suited for power users who are familiar with command line programs. | |
| py-s3transfer | S3transfer is a Python library for managing Amazon S3 transfers. | |
| py-scikit-image | Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. | |
| py-scikit-learn-extra | A set of useful tools compatible with scikit-learn | |
| py-scikit-learn | A set of python modules for machine learning and data mining. | |
| py-scipy | SciPy (pronounced Sigh Pie) is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. | |
| py-screed | FIXME: Put a proper description of your package here. | |
| py-send2trash | Python library to send files to Trash/Recycle on all platforms. | |
| py-setuptools-scm-git-archive | This is a setuptools_scm plugin that adds support for git archives (for example the ones GitHub automatically generates). | |
| py-setuptools-scm | The blessed package to manage your versions by scm tags. | |
| py-setuptools | A Python utility that aids in the process of downloading, building, upgrading, installing, and uninstalling Python packages. | |
| py-simplegeneric | Simple generic functions (similar to Pythons own len(), pickle.dump(), etc.) | |
| py-simplejson | Simplejson is a simple, fast, extensible JSON encoder/decoder for Python | |
| py-simplesam | Simple pure Python SAM parser and objects for working with SAM records | |
| py-sip | A Python bindings generator for C/C++ libraries. | |
| py-six | Python 2 and 3 compatibility utilities. | |
| py-smart-open | smart_open is a Python 2 Python 3 library for efficient streaming of very large files from/to S3, HDFS, WebHDFS, HTTP, or local storage. It supports transparent, on-the-fly (de-)compression for a variety of different formats. | |
| py-smartypants | smartypants is a Python fork of SmartyPants. | |
| py-smmap | A pure Python implementation of a sliding window memory map manager | |
| py-sniffio | This is a tiny package whose only purpose is to let you detect which async library your code is running under. | |
| py-snowballstemmer | This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowball algorithms. | |
| py-sortedcontainers | Sorted Containers is an Apache2 licensed sorted collections library, written in pure-Python, and fast as C-extensions. | |
| py-soupsieve | A modern CSS selector implementation for Beautiful Soup. | |
| py-spectra | Color scales and color conversion made easy for Python. | |
| py-spglib | Python bindings for C library for finding and handling crystal symmetries. | |
| py-sphinx | Sphinx Documentation Generator. | |
| py-sphinxcontrib-applehelp | sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books. | |
| py-sphinxcontrib-devhelp | sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document. | |
| py-sphinxcontrib-htmlhelp | sphinxcontrib-htmlhelp is a sphinx extension which outputs htmlhelp document. | |
| py-sphinxcontrib-jsmath | A sphinx extension which renders display math in HTML via JavaScript. | |
| py-sphinxcontrib-qthelp | sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document. | |
| py-sphinxcontrib-serializinghtml | sphinxcontrib-serializinghtml is a sphinx extension which outputs serialized HTML files (json and pickle). | |
| py-stack-data | Extract data from python stack frames and tracebacks for informative displays. | |
| py-statsmodels | Statistical computations and models for use with SciPy | |
| py-stopit | Raise asynchronous exceptions in other threads, control the timeout of blocks or callables with two context managers and two decorators. | |
| py-tabulate | Pretty-print tabular data | |
| py-tblib | Traceback fiddling library. Allows you to pickle tracebacks. | |
| py-telomeracat | Extensions to the Python standard library unit testing framework. | |
| py-tenacity | Retrying library for Python | |
| py-tensorboard-data-server | Fast data loading for TensorBoard | |
| py-tensorboard-plugin-wit | The What-If Tool makes it easy to efficiently and intuitively explore up to two models performance on a dataset. Investigate model performances for a range of features in your dataset, optimization strategies and even manipulations to individual datapoint values. All this and more, in a visual way that requires minimal code. | |
| py-tensorboard | TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs. | |
| py-tensorflow | An Open Source Machine Learning Framework for Everyone. | |
| py-termcolor | ANSII Color formatting for output in terminal. | |
| py-terminado | Terminals served to term.js using Tornado websockets | |
| py-testpath | Testpath is a collection of utilities for Python code working with files and commands. | |
| py-threadpoolctl | Python helpers to limit the number of threads used in the threadpool-backed of common native libraries used for scientific computing and data science (e.g. BLAS and OpenMP). | |
| py-tifffile | Read and write image data from and to TIFF files. | |
| py-toml | A Python library for parsing and creating TOML configuration files. For more information on the TOML standard, see https://github.com/toml-lang/toml.git | |
| py-tomli-w | A lil TOML writer. | |
| py-tomli | Tomli is a Python library for parsing TOML. | |
| py-tomlkit | Style preserving TOML library | |
| py-toolz | A set of utility functions for iterators, functions, and dictionaries | |
| py-toposort | Implements a topological sort algorithm. | |
| py-torch | Tensors and Dynamic neural networks in Python with strong GPU acceleration. | |
| py-tornado | Tornado is a Python web framework and asynchronous networking library. | |
| py-tqdm | A Fast, Extensible Progress Meter | |
| py-traitlets | Traitlets Python config system | |
| py-twisted | An asynchronous networking framework written in Python | |
| py-typing-extensions | The typing_extensions module contains both backports of these changes as well as experimental types that will eventually be added to the typing module, such as Protocol (see PEP 544 for details about protocols and static duck typing). | |
| py-unicycler | Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly. | |
| py-uritemplate | Simple python library to deal with URI Templates. | |
| py-urllib3 | HTTP library with thread-safe connection pooling, file post, and more. | |
| py-virtualenv | virtualenv is a tool to create isolated Python environments. | |
| py-voluptuous | Voluptous, despite the name, is a Python data validation library. | |
| py-wcwidth | Measures number of Terminal column cells of wide-character codes | |
| py-webencodings | This is a Python implementation of the WHATWG Encoding standard. | |
| py-websocket-client | WebSocket client for Python. hybi13 is supported. | |
| py-werkzeug | The Swiss Army knife of Python web development | |
| py-wheel | A built-package format for Python. | |
| py-widgetsnbextension | IPython HTML widgets for Jupyter | |
| py-wrapt | Module for decorators, wrappers and monkey patching. | |
| py-wxpython | Cross platform GUI toolkit for Python. | |
| py-xopen | This small Python module provides a xopen function that works like the built-in open function, but can also deal with compressed files. Supported compression formats are gzip, bzip2 and xz. They are automatically recognized by their file extensions .gz, .bz2 or .xz. | |
| py-zict | Mutable mapping tools | |
| py-zipp | Backport of pathlib-compatible object wrapper for zip files. | |
| py-zope-interface | This package provides an implementation of object interfaces for Python. Interfaces are a mechanism for labeling objects as conforming to a given API or contract. So, this package can be considered as implementation of the Design By Contract methodology support in Python. | |
| py | ||
| pyfits | ||
| pygtk | ||
| pymol | ||
| pypy | ||
| pyqt | ||
| python | python | The Python programming language. |
| python26-modules | ||
| python27-modules | ||
| python34-modules | ||
| python36-modules | ||
| pytorch |
Q
| module name | link to docs | description |
|---|---|---|
| qe | ||
| qe_rism | ||
| qhull | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furt hest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull. | |
| qiime | qiime | |
| qrupdate | qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. | |
| qscintilla | QScintilla is a port to Qt of Neil Hodgsons Scintilla C++ editor control. | |
| qt | ||
| qualimap | ||
| quantum-espresso | quantum-espresso | Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. |
| quast | ||
| quorum |
R
| module name | link to docs | description |
|---|---|---|
| r-abind | Combine multidimensional arrays into a single array. This is a generalization of cbind and rbind. Works with vectors, matrices, and higher-dimensional arrays. Also provides functions adrop, asub, and afill for manipulating, extracting and replacing data in arrays. | |
| r-amap | Another Multidimensional Analysis Package. | |
| r-annotate | Annotation for microarrays. | |
| r-annotationdbi | Manipulation of SQLite-based annotations in Bioconductor. | |
| r-ape | Analyses of Phylogenetics and Evolution. | |
| r-argparse | A command line parser to be used with Rscript to write ! shebang scripts that gracefully accept positional and optional arguments and automatically generate usage. | |
| r-askpass | Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no tcltk is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for ssh-agent or git-credential via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh. | |
| r-assertthat | assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what theyve done wrong. | |
| r-backports | Implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version. | |
| r-base64enc | This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package. | |
| r-bayesplot | Plotting for Bayesian Models. | |
| r-bh | Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN package. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. As of release 1.60.0-2, the following Boost libraries are included: algorithm any bimap bind circular_buffer concept config container date_time detail dynamic_bitset exception filesystem flyweight foreach functional fusion geometry graph heap icl integer interprocess intrusive io iostreams iterator math move mpl multiprcecision numeric pending phoenix preprocessor random range smart_ptr spirit tuple type_trains typeof unordered utility uuid. | |
| r-biasedurn | Biased Urn Model Distributions. | |
| r-bigmemory-sri | A shared resource interface for Bigmemory Project packages. | |
| r-bigmemory | Manage Massive Matrices with Shared Memory and Memory-Mapped. | |
| r-binom | Parametrized Active Bindings. | |
| r-biobase | Biobase: Base functions for Bioconductor. | |
| r-biocfilecache | Manage Files Across Sessions. | |
| r-biocgenerics | S4 generic functions used in Bioconductor. | |
| r-biocio | Standard Input and Output for Bioconductor Packages. | |
| r-biocmanager | BiocManager: Access the Bioconductor Project Package Repository | |
| r-biocparallel | Bioconductor facilities for parallel evaluation. | |
| r-biomart | Interface to BioMart databases (i.e. Ensembl). | |
| r-biostrings | Efficient manipulation of biological strings. | |
| r-bit | Classes and Methods for Fast Memory-Efficient Boolean Selections. | |
| r-bit64 | A S3 Class for Vectors of 64bit Integers. | |
| r-bitops | Bitwise Operations. | |
| r-blob | A Simple S3 Class for Representing Vectors of Binary Data (BLOBS). | |
| r-brew | brew implements a templating framework for mixing text and R code for report generation. brew template syntax is similar to PHP, Rubys erb module, Java Server Pages, and Pythons psp module. | |
| r-bridgesampling | Bridge Sampling for Marginal Likelihoods and Bayes Factors. | |
| r-brio | Basic R Input Output. | |
| r-brms | Bayesian Regression Models using Stan. | |
| r-brobdingnag | Very Large Numbers in R. | |
| r-broom | Convert Statistical Objects into Tidy Tibbles. | |
| r-bsgenome | Software infrastructure for efficient representation of full genomes and their SNPs. | |
| r-bslib | Custom Bootstrap Sass Themes for shiny and rmarkdown. | |
| r-cachem | Cache R Objects with Automatic Pruning. | |
| r-callr | It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that. | |
| r-caret | Misc functions for training and plotting classification and regression models. | |
| r-catools | Moving Window Statistics, GIF, Base64, ROC AUC, etc. | |
| r-cellranger | Helper functions to work with spreadsheets and the A1:D10 style of cell range specification. | |
| r-checkmate | Fast and Versatile Argument Checks. | |
| r-class | Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps. | |
| r-classint | Choose Univariate Class Intervals. | |
| r-cli | A suite of tools designed to build attractive command line interfaces (CLIs). Includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives. | |
| r-clipr | Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards. | |
| r-clisymbols | A small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode. Many symbols were taken from the figures npm package (see https://github.com/sindresorhus/figures). | |
| r-cluster | Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) Finding Groups in Data. | |
| r-clustergeneration | Random Cluster Generation (with Specified Degree of Separation). | |
| r-cmdstanr | R Interface to CmdStan. | |
| r-coda | Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain. | |
| r-codetools | Code analysis tools for R. | |
| r-colorspace | Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided. | |
| r-colourpicker | A Colour Picker Tool for Shiny and for Selecting Colours in Plots. | |
| r-combinat | combinatorics utilities. | |
| r-commonmark | commonmark: CommonMark and Github Markdown Rendering in R | |
| r-corpcor | Efficient Estimation of Covariance and (Partial) Correlation | |
| r-covr | Test Coverage for Packages. | |
| r-cpp11 | A C++11 Interface for Rs C Interface. | |
| r-crayon | Colored terminal output on terminals that support ANSI color and highlight codes. It also works in Emacs ESS. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the chalk JavaScript project. | |
| r-credentials | Tools for Managing SSH and Git Credentials. | |
| r-crosstalk | Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). | |
| r-ctc | Cluster and Tree Conversion. | |
| r-curl | The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of libcurl is recommended; for a more-user-friendly web client see the httr package which builds on this package with http specific tools and logic. | |
| r-dada2 | Accurate sample inference from amplicon data with single nucleotide resolution | |
| r-data-table | Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible syntax, for faster development. | |
| r-dbi | R Database Interface. | |
| r-dbplyr | A dplyr Back End for Databases. | |
| r-delayedarray | A unified framework for working transparently with on-disk and in-memory array-like datasets. | |
| r-deldir | Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation. | |
| r-deoptimr | An implementation of a bespoke jDE variant of the Differential Evolution stochastic algorithm for global optimization of nonlinear programming problems. | |
| r-desc | desc: Manipulate DESCRIPTION Files | |
| r-deseq | Differential gene expression analysis based on the negative binomial distribution. | |
| r-deseq2 | Differential gene expression analysis based on the negative binomial distribution. | |
| r-desolve | Solvers for Initial Value Problems of Differential Equations (ODE, DAE, DDE). | |
| r-devtools | Collection of package development tools. | |
| r-diffobj | Diffs for R Objects. | |
| r-digest | Implementation of a function digest() for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function hmac() to create hash-based message authentication code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described in ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1, sha-256 and aes, this package uses small standalone implementations that were provided by Christophe Devine. For crc32, code from the zlib library is used. For sha-512, an implementation by Aaron D. Gifford is used. For xxhash, the implementation by Yann Collet is used. For murmurhash, an implementation by Shane Day is used. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used. | |
| r-distributional | Functions for Base Types and Core R and Tidyverse Features. | |
| r-doparallel | Foreach Parallel Adaptor for the parallel Package. | |
| r-dplyr | A fast, consistent tool for working with data frame like objects, both in memory and out of memory. | |
| r-dt | Data objects in R can be rendered as HTML tables using the JavaScript library DataTables (typically via R Markdown or Shiny). The DataTables library has been included in this R package. The package name DT is an abbreviation of DataTables. | |
| r-dtplyr | Data Table Back-End for dplyr. | |
| r-dygraphs | Interface to Dygraphs Interactive Time Series Charting Library. | |
| r-e1071 | Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien. | |
| r-edger | Empirical Analysis of Digital Gene Expression Data in R. | |
| r-ellipsis | The ellipsis is a powerful tool for extending functions. Unfortunately this power comes at a cost: misspelled arguments will be silently ignored. The ellipsis package provides a collection of functions to catch problems and alert the user. | |
| r-ergm | An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). ergm is a part of the statnet suite of packages for network analysis. | |
| r-evaluate | Parsing and evaluation tools that make it easy to recreate the command line behaviour of R. | |
| r-expm | Matrix Exponential, Log, etc. | |
| r-fansi | Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences. | |
| r-farver | High Performance Colour Space Manipulation. | |
| r-fastcluster | Fast Hierarchical Clustering Routines for R and Python. | |
| r-fastmap | Fast Implementation of a Key-Value Store. | |
| r-fastmatch | Fast match() Function. | |
| r-filelock | Portable File Locking. | |
| r-findpython | Package designed to find an acceptable python binary. | |
| r-fontawesome | Easily Work with Font Awesome Icons. | |
| r-forcats | Tools for Working with Categorical Variables (Factors). | |
| r-foreach | Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesnt require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel. | |
| r-formatr | Format R Code Automatically. | |
| r-fs | A cross-platform interface to file system operations, built on top of the libuv C library. | |
| r-futile-logger | A Logging Utility for R. | |
| r-futile-options | Futile Options Management. | |
| r-future-apply | Apply Function to Elements in Parallel using Futures. | |
| r-future | Unified Parallel and Distributed Processing in R for Everyone. | |
| r-gargle | Utilities for Working with Google APIs. | |
| r-geiger | Analysis of Evolutionary Diversification. | |
| r-genefilter | Methods for filtering genes from high-throughput experiments. | |
| r-genelendatabase | Lengths of mRNA transcripts for a number of genomes. | |
| r-geneplotter | Graphics related functions for Bioconductor. | |
| r-generics | In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics. | |
| r-genomeinfodb | Utilities for manipulating chromosome names, including modifying them to follow a particular naming style. | |
| r-genomeinfodbdata | for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package. | |
| r-genomicalignments | Representation and manipulation of short genomic alignments. | |
| r-genomicfeatures | Conveniently import and query gene models. | |
| r-genomicranges | Representation and manipulation of genomic intervals. | |
| r-gert | Simple Git Client for R. | |
| r-getopt | C-Like getopt Behavior. | |
| r-ggdendro | Create Dendrograms and Tree Diagrams Using ggplot2. | |
| r-ggplot2 | An implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes. See http://ggplot2.org for more information, documentation and examples. | |
| r-ggridges | Ridgeline Plots in ggplot2. | |
| r-gh | Minimal client to access the GitHub API. | |
| r-git2r | Interface to the libgit2 library, which is a pure C implementation of the Git core methods. Provides access to Git repositories to extract data and running some basic Git commands. | |
| r-gitcreds | Query git Credentials from R. | |
| r-glimma | Interactive HTML graphics. | |
| r-globals | Identify Global Objects in R Expressions. | |
| r-glue | An implementation of interpreted string literals, inspired by Pythons Literal String Interpolation https://www.python.org/dev/peps/pep-0498/ and Docstrings https://www.python.org/dev/peps/pep-0257/ and Julias Triple-Quoted String Literals [https://docs.julialang.org/en/stable/ manual/strings/triple-quoted-string-literals](https://docs.julialang.org/en/stable/ manual/strings/triple-quoted-string-literals). | |
| r-gmp | Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), arithmetic without limitations using the C library GMP (GNU Multiple Precision Arithmetic). | |
| r-go-db | A set of annotation maps describing the entire Gene Ontology. | |
| r-goftest | Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for continuous univariate distributions, using efficient algorithms. | |
| r-googledrive | An Interface to Google Drive. | |
| r-googlesheets4 | Access Google Sheets using the Sheets API V4. | |
| r-goplot | Visualization of Functional Analysis Data. | |
| r-goseq | Gene Ontology analyser for RNA-seq and other length biased data. | |
| r-gower | Compute Gowers distance (or similarity) coefficient between records. Compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP. | |
| r-gplots | Various R Programming Tools for Plotting Data. | |
| r-gridextra | Miscellaneous Functions for Grid Graphics. | |
| r-gtable | Tools to make it easier to work with tables of grobs. | |
| r-gtools | Various R Programming Tools. | |
| r-haven | Import and Export SPSS, Stata and SAS Files. | |
| r-here | A Simpler Way to Find Your Files. | |
| r-highr | Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simons highlight package. | |
| r-hms | Implements an S3 class for storing and formatting time-of-day values, based on the difftime class. | |
| r-htmltools | Tools for HTML generation and output. | |
| r-htmlwidgets | A framework for creating HTML widgets that render in various contexts including the R console, R Markdown documents, and Shiny web applications. | |
| r-httpuv | Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.) | |
| r-httr | Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on). | |
| r-hwriter | HTML Writer - Outputs R objects in HTML format. | |
| r-ids | Generate Random Identifiers. | |
| r-igraph | Network Analysis and Visualization. | |
| r-ini | Parse simple .ini configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications. | |
| r-inline | Functions to Inline C, C++, Fortran Function Calls from R. | |
| r-ipred | Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error. | |
| r-iranges | Foundation of integer range manipulation in Bioconductor. | |
| r-irdisplay | An interface to the rich display capabilities of Jupyter front-ends (e.g. Jupyter Notebook) Designed to be used from a running IRkernel session | |
| r-irkernel | Native R Kernel for the Jupyter Notebook. | |
| r-isoband | Generate Isolines and Isobands from Regularly Spaced Elevation Grids. | |
| r-iterators | Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data. | |
| r-jpeg | Read and write JPEG images. | |
| r-jquerylib | Obtain jQuery as an HTML Dependency Object. | |
| r-jsonlite | A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of RJSONIO, but has been completely rewritten in recent versions. The package offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, jsonlite contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications. | |
| r-keggrest | Client-side REST access to KEGG. | |
| r-kernsmooth | Functions for kernel smoothing (and density estimation). | |
| r-knitr | Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques. | |
| r-labeling | Provides a range of axis labeling algorithms. | |
| r-lambda-r | Modeling Data with Functional Programming. | |
| r-later | Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. | |
| r-lattice | A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction. | |
| r-latticeextra | Extra Graphical Utilities Based on Lattice. | |
| r-lava | Estimation and simulation of latent variable models. | |
| r-lazyeval | An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style quasiquotation, making it easier to generate code with other code. | |
| r-lhs | Latin Hypercube Samples. | |
| r-lifecycle | Manage the Life Cycle of your Package Functions. | |
| r-limma | Linear Models for Microarray Data. | |
| r-listenv | Environments Behaving (Almost) as Lists. | |
| r-locfit | Local regression, likelihood and density estimation. | |
| r-loo | Efficient Leave-One-Out Cross-Validation and WAIC for BayesianModels. | |
| r-lpsolve | Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a wrapper function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve | |
| r-lubridate | Functions to work with date-times and timespans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and timespan objects. The lubridate package has a consistent and memorable syntax that makes working with dates easy and fun. | |
| r-magrittr | Provides a mechanism for chaining commands with a new forward-pipe operator, . This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. | |
| r-maps | Draw Geographical Maps. | |
| r-markdown | Provides R bindings to the Sundown Markdown rendering library (https://github.com/vmg/sundown). Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats. See http://en.wikipedia.org/wiki/Markdown for more information about Markdown. | |
| r-mass | Functions and datasets to support Venables and Ripley, Modern Applied Statistics with S (4th edition, 2002). | |
| r-matrix | Classes and methods for dense and sparse matrices and operations on them using LAPACK and SuiteSparse. | |
| r-matrixgenerics | S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects. | |
| r-matrixstats | Functions that Apply to Rows and Columns of Matrices (and to Vectors). | |
| r-memoise | Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value. | |
| r-mgcv | GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family. | |
| r-mime | Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems. | |
| r-miniui | Shiny UI Widgets for Small Screens. | |
| r-mnormt | The Multivariate Normal and t Distributions, and Their Truncated Versions. | |
| r-modelmetrics | Collection of metrics for evaluating models written in C++ using Rcpp. | |
| r-modelr | Modelling Functions that Work with the Pipe. | |
| r-munsell | Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsells original notation (e.g. 5R 5/10) and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes. | |
| r-mvtnorm | Multivariate Normal and t Distributions. | |
| r-ncbit | Retrieve and build NBCI taxonomic data. | |
| r-ncdf4 | Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files. | |
| r-network | Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes. | |
| r-nleqslv | Solve Systems of Nonlinear Equations. | |
| r-nlme | Fit and compare Gaussian linear and nonlinear mixed-effects models. | |
| r-nloptr | R Interface to NLopt. | |
| r-nnet | Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models. | |
| r-numderiv | Methods for calculating (usually) accurate numerical first and second order derivatives. | |
| r-openssl | Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and bignum math methods for manually performing crypto calculations on large multibyte integers. | |
| r-optparse | Command Line Option Parser. | |
| r-packrat | A Dependency Management System for Projects and their R Package Dependencies. | |
| r-paleotree | Paleontological and Phylogenetic Analyses of Evolution. | |
| r-parallelly | Enhancing the parallel Package. | |
| r-pbdzmq | ZeroMQ is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize ZeroMQ. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal ZeroMQ library (4.1.0 rc1) is shipped with pbdZMQ, which can be used if no system installation of ZeroMQ is available. A few wrapper functions compatible with rzmq are also provided. | |
| r-permute | A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. permute also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The permute package is modelled after the permutation schemes of Canoco 3.1 (and later) by Cajo ter Braak. | |
| r-phangorn | Phylogenetic Reconstruction and Analysis. | |
| r-phytools | Phylogenetic Tools for Comparative Biology (and Other Things). | |
| r-pillar | Provides a pillar generic designed for formatting columns of data using the full range of colours provided by modern terminals. | |
| r-pkgbuild | pkgbuild: Find Tools Needed to Build R Packages | |
| r-pkgconfig | Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected. | |
| r-pkgload | pkgload: Simulate Package Installation and Attach | |
| r-plogr | A simple header-only logging library for C++. Add LinkingTo: plogr to DESCRIPTION, and include plogr.h in your C++ modules to use it. | |
| r-plotly | Create Interactive Web Graphics via plotly.js. | |
| r-plotrix | Various Plotting Functions. | |
| r-plyr | A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of plyr has been generously supported by Becton Dickinson. | |
| r-png | Read and write PNG images. | |
| r-polyclip | polyclip: Polygon Clipping | |
| r-posterior | Tools for Working with Posterior Distributions. | |
| r-praise | Build friendly R packages that praise their users if they have done something good, or they just need it to feel better. | |
| r-prettyunits | Pretty, human readable formatting of quantities. Time intervals: 1337000 - 15d 11h 23m 20s. Vague time intervals: 2674000 - about a month ago. Bytes: 1337 - 1.34 kB. | |
| r-processx | Tools to run system processes in the background | |
| r-prodlim | Product-Limit Estimation for Censored Event History Analysis. Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method. | |
| r-progress | Configurable Progress bars, they may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in Emacs ESS, RStudio, Windows Rgui and the macOS R.app. The package also provides a C++ API, that works with or without Rcpp. | |
| r-promises | Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to JavaScript promises, but with a syntax that is idiomatic R. | |
| r-proto | An object oriented system using object-based, also called prototype-based, rather than class-based object oriented ideas. | |
| r-proxy | Distance and Similarity Measures. | |
| r-ps | Manipulate processes on Windows, Linux and MacOS | |
| r-ptw | Parametric Time Warping. | |
| r-purrr | A complete and consistent functional programming toolkit for R. | |
| r-quadprog | Functions to Solve Quadratic Programming Problems. | |
| r-qvalue | Q-value estimation for false discovery rate control. | |
| r-r6 | The R6 package allows the creation of classes with reference semantics, similar to Rs built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages. | |
| r-rappdirs | Application Directories: Determine Where to Save Data, Caches, and Logs. | |
| r-raster | Geographic Data Analysis and Modeling. | |
| r-rcmdcheck | Run R CMD check from R and capture the results of the individual checks. Supports running checks in the background, timeouts, pretty printing and comparing check results. | |
| r-rcolorbrewer | Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org | |
| r-rcpp | The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see citation(Rcpp) for details on these last two. | |
| r-rcpparmadillo | Rcpp Integration for the Armadillo Templated Linear Algebra Library. | |
| r-rcppde | Global Optimization by Differential Evolution in C++. | |
| r-rcppeigen | R and Eigen integration using Rcpp. Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on Lapack and level-3 BLAS. The RcppEigen package includes the header files from the Eigen C++ template library (currently version 3.2.8). Thus users do not need to install Eigen itself in order to use RcppEigen. Since version 3.1.1, Eigen is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. RcppEigen (the Rcpp bindings/bridge to Eigen) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp. | |
| r-rcppparallel | Parallel Programming Tools for Rcpp. | |
| r-rcpptoml | Rcpp Bindings to Parser for Toms Obvious Markup Language. | |
| r-rcurl | General Network (HTTP/FTP/…) Client Interface for R. | |
| r-readr | Read Rectangular Text Data. | |
| r-readxl | Import excel files into R. Supports .xls via the embedded libxls C library https://sourceforge.net/projects/libxls/ and .xlsx via the embedded RapidXML C++ library https://rapidxml.sourceforge.net. Works on Windows, Mac and Linux without external dependencies. | |
| r-recipes | An extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis steps. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models. | |
| r-rematch | A small wrapper on regexpr to extract the matches and captured groups from the match of a regular expression to a character vector. | |
| r-rematch2 | Tidy Output from Regular Expression Matching. | |
| r-remotes | Download and install R packages stored in GitHub, BitBucket, or plain subversion or git repositories. This package provides the install_* functions in devtools. Indeed most of the code was copied over from devtools. | |
| r-repr | String and binary representations of objects for several formats and mime types. | |
| r-reprex | Prepare Reproducible Example Code via the Clipboard. | |
| r-reshape2 | Flexibly restructure and aggregate data using just two functions: melt and dcast (or acast). | |
| r-restfulr | R Interface to RESTful Web Services. | |
| r-reticulate | Interface to Python. | |
| r-rex | Friendly Regular Expressions. | |
| r-rgl | 3D Visualization Using OpenGL. | |
| r-rhtslib | HTSlib high-throughput sequencing library as an R package. | |
| r-rinside | C++ Classes to Embed R in C++ (and C) Applications. | |
| r-rjson | JSON for R. | |
| r-rlang | A toolbox for working with base types, core R features like the condition system, and core Tidyverse features like tidy evaluation. | |
| r-rmarkdown | Dynamic Documents for R. | |
| r-rmpfr | Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental (special) functions. To this end, Rmpfr interfaces to the LGPLed MPFR (Multiple Precision Floating-Point Reliable) Library which itself is based on the GMP (GNU Multiple Precision) Library. | |
| r-rmpi | Interface (Wrapper) to MPI (Message-Passing Interface). | |
| r-robustbase | Essential Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book Robust Statistics, Theory and Methods by Maronna, Martin and Yohai; Wiley 2006. | |
| r-rots | Reproducibility-Optimized Test Statistic. | |
| r-roxygen2 | A Doxygen-like in-source documentation system for Rd, collation, and NAMESPACE files. | |
| r-rpart-plot | Plot rpart models. Extends plot.rpart() and text.rpart() in the rpart package. | |
| r-rpart | Recursive partitioning for classification, regression and survival trees. | |
| r-rprojroot | Robust, reliable and flexible paths to files below a project root. The root of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file. | |
| r-rsamtools | Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. | |
| r-rsconnect | Deployment Interface for R Markdown Documents and Shiny Applications. | |
| r-rsqlite | SQLite Interface for R. | |
| r-rstan | R Interface to Stan. | |
| r-rstantools | Tools for Developing R Packages Interfacing with Stan. | |
| r-rstudioapi | Access the RStudio API (if available) and provide informative error messages when its not. | |
| r-rtracklayer | R interface to genome annotation files and the UCSC genome browser. | |
| r-rversions | Query R Versions, Including r-release and r-oldrel. | |
| r-rvest | Easily Harvest (Scrape) Web Pages. | |
| r-s2 | Spherical Geometry Operators Using the S2 Geometry Library. | |
| r-s4vectors | Foundation of vector-like and list-like containers in Bioconductor. | |
| r-sass | Syntactically Awesome Style Sheets (Sass). | |
| r-scales | Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends. | |
| r-scatterplot3d | 3D Scatter Plot. | |
| r-selectr | Translate CSS Selectors to XPath Expressions. | |
| r-seqlogo | Sequence logos for DNA sequence alignments. | |
| r-sessioninfo | Query and print information about the current R session. It is similar to utils::sessionInfo(), but includes more information about packages, and where they were installed from. | |
| r-sf | Simple Features for R. | |
| r-shiny | Makes it incredibly easy to build interactive web applications with R. Automatic reactive binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort. | |
| r-shinyjs | Easily Improve the User Experience of Your Shiny Apps in Seconds. | |
| r-shinystan | Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models. | |
| r-shinythemes | Themes for Shiny. | |
| r-shortread | FASTQ input and manipulation. | |
| r-sm | Smoothing Methods for Nonparametric Regression and Density Estimation. | |
| r-snow | Simple Network of Workstations. | |
| r-sourcetools | Tools for Reading, Tokenizing and Parsing R Code. | |
| r-sp | Classes and Methods for Spatial Data. | |
| r-spatstat-data | Contains all the datasets for the spatstat package. | |
| r-spatstat-utils | Contains utility functions for the spatstat package which may also be useful for other purposes. | |
| r-spatstat | Comprehensive open-source toolbox for analysing Spatial Point Patterns. | |
| r-squarem | Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette(SQUAREM). | |
| r-stanheaders | C++ Header Files for Stan. | |
| r-statnet-common | Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others. | |
| r-stringi | Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, etc. | |
| r-stringr | A consistent, simple and easy to use set of wrappers around the fantastic stringi package. All function and argument names (and positions) are consistent, all functions deal with NAs and zero length vectors in the same way, and the output from one function is easy to feed into the input of another. | |
| r-subplex | Unconstrained Optimization using the Subplex Algorithm. | |
| r-summarizedexperiment | SummarizedExperiment container. | |
| r-survival | Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models. | |
| r-sys | Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales. | |
| r-tensor | The tensor product of two arrays is notionally an outer product of the arrays collapsed in specific extents by summing along the appropriate diagonals. | |
| r-tensora | Advanced Tensor Arithmetic with Named Indices. | |
| r-terra | Spatial Data Analysis. | |
| r-testthat | A unit testing system designed to be fun, flexible and easy to set up. | |
| r-threejs | Interactive 3D Scatter Plots, Networks and Globes. | |
| r-tibble | Provides a tbl_df class that offers better checking and printing capabilities than traditional data frames. | |
| r-tidyr | An evolution of reshape2. Its designed specifically for data tidying (not general reshaping or aggregating) and works well with dplyr data pipelines. | |
| r-tidyselect | A backend for the selecting functions of the tidyverse. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other tidyverse interfaces for selection. | |
| r-tidyverse | Easily Install and Load the Tidyverse. | |
| r-timedate | Environment for teaching Financial Engineering and Computational Finance. Managing chronological and calendar objects. | |
| r-tinytex | Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents. | |
| r-tmvnsim | Truncated Multivariate Normal Simulation. | |
| r-trust | Does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function. | |
| r-tzdb | Time Zone Database Information. | |
| r-udunits2 | Provides simple bindings to Unidatas udunits library. | |
| r-units | Measurement Units for R Vectors. | |
| r-usethis | Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, GitHub, licenses, Rcpp, RStudio projects, and more. | |
| r-utf8 | Process and print UTF-8 encoded international text (Unicode). Input, validate, normalize, encode, format, and display. | |
| r-uuid | Tools for generating and handling of UUIDs (Universally Unique Identifiers). | |
| r-vctrs | Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analyzing function interfaces. | |
| r-vegan | Ordination methods, diversity analysis and other functions for community and vegetation ecologists. | |
| r-viridislite | viridisLite: Default Color Maps from matplotlib (Lite Version) | |
| r-vroom | Read and Write Rectangular Text Data Quickly. | |
| r-waldo | Find Differences Between R Objects. | |
| r-whisker | logicless templating, reuse templates in many programming languages including R | |
| r-withr | A set of functions to run code with safely and temporarily modified global state. Many of these functions were originally a part of the devtools package, this provides a simple package with limited dependencies to provide access to these functions. | |
| r-wk | Lightweight Well-Known Geometry Parsing. | |
| r-xfun | Miscellaneous functions commonly used in other packages maintained by Yihui Xie. | |
| r-xml | Tools for Parsing and Generating XML Within R and S-Plus. | |
| r-xml2 | Work with XML files using a simple, consistent interface. Built on top of the libxml2 C library. | |
| r-xopen | Cross platform solution to open files, directories or URLs with their associated programs. | |
| r-xtable | Coerce data to LaTeX and HTML tables. | |
| r-xts | eXtensible Time Series. | |
| r-xvector | Foundation of external vector representation and manipulation in Bioconductor. | |
| r-yaml | This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R. | |
| r-zeallot | Provides a - operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment. | |
| r-zip | Cross-Platform zip Compression. | |
| r-zlibbioc | An R packaged zlib-1.2.5. | |
| r-zoo | S3 Infrastructure for Regular and Irregular Time Series (Zs Ordered Observations). | |
| r | r | R is GNU S, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information. |
| r8s | ||
| ra | ||
| rabifier | ||
| racon | ||
| rainbow | ||
| randrproto | X Resize and Rotate Extension (RandR). | |
| rapidjson | A fast JSON parser/generator for C++ with both SAX/DOM style API | |
| ratatosk | ||
| raven | ||
| raxml-ng | ||
| raxml | RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. | |
| ray | ||
| rcorrector | ||
| rdkit | ||
| rdma-core | RDMA core userspace libraries and daemons | |
| re2 | RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. | |
| re2c | re2c: a free and open-source lexer generator for C and C++ | |
| readline | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. | |
| recordproto | X Record Extension. | |
| redundans | ||
| relion | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). | |
| renderproto | X Rendering Extension. | |
| repeatexplorer | ||
| repeatmasker | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | |
| repeatmodeler | ||
| repeatprofiler | ||
| repliscan | ||
| respect | ||
| revbayes | revbayes | Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language. |
| rmats | ||
| rnaframework | ||
| rnastructure | ||
| rngstreams | Multiple independent streams of pseudo-random numbers. | |
| root | ||
| rosetta | rosetta | |
| rosettafold | ||
| rpcsvc-proto | rpcsvc protocol definitions from glibc. | |
| rsem | ||
| rseqc | ||
| rsh-to | ||
| rstudio | rstudio | |
| ruby | A dynamic, open source programming language with a focus on simplicity and productivity. | |
| rust | The Rust programming language toolchain |
S
| module name | link to docs | description |
|---|---|---|
| saga | ||
| sagemath | ||
| salmon | Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. | |
| samblaster | ||
| samtools | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format | |
| saws | The Scientific Application Web server (SAWs) turns any C or C++ scientific or engineering application code into a webserver, allowing one to examine (and even modify) the state of the simulation with any browser from anywhere. | |
| scalapack | ||
| scallop | Scallop is a reference-based transcriptome assembler for RNA-seq | |
| scanmatches | ||
| scientificpython | ||
| scipion | ||
| scipy | ||
| scons | SCons is a software construction tool | |
| scotch | Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering. | |
| scrnsaverproto | MIT Screen Saver Extension. | |
| sdl | ||
| sdl2 | Simple DirectMedia Layer is a cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D. | |
| seacas | The SEACAS Project contains the Exodus and IOSS libraries and a collection of applications which create, query, modify, or translate exodus databases. Default is to build the exodus and IOSS libraries and the io_shell, io_info, io_modify, struc_to_unstruc apps. | |
| sed | GNU implementation of the famous stream editor. | |
| seecer | ||
| seqtk | ||
| seqtools | ||
| serf | Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library | |
| serpent | ||
| setuptools | ||
| sga | ||
| shapeit4 | SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. | |
| shared-mime-info | Database of common MIME types. | |
| siesta | SIESTA performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. | |
| signalalign | ||
| singul | ||
| sip | ||
| sklearn | ||
| slr | ||
| smilei | ||
| snakemake | snakemake | Snakemake is an MIT-licensed workflow management system. |
| snap-korf | SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. | |
| snap | SNAP serves as a proxy application to model the performance of a modern discrete ordinates neutral particle transport application. SNAP may be considered an update to Sweep3D, intended for hybrid computing architectures. It is modeled off the Los Alamos National Laboratory code PARTISN. | |
| snapp | ||
| snappy | A fast compressor/decompressor: https://code.google.com/p/snappy | |
| sniffles | ||
| snpeff | SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). | |
| snphylo | ||
| soap | ||
| soapalign | ||
| soapdenovo-trans | ||
| soapdenovo2 | SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. | |
| soci | Official repository of the SOCI - The C++ Database Access Library | |
| solve | ||
| sortmerna | SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data | |
| sox | ||
| spades | spades | SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. |
| sparsehash | Sparse and dense hash-tables for C++ by Google | |
| sparx | ||
| spdlog | Very fast, header only, C++ logging library | |
| spectre | ||
| speex | Speex is an Open Source/Free Software patent-free audio compression format designed for speech. | |
| spfft | Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support. | |
| spglib | C library for finding and handling crystal symmetries. | |
| spla | Specialized Parallel Linear Algebra, providing distributed GEMM functionality for specific matrix distributions with optional GPU acceleration. | |
| spython | ||
| sqlite | SQLite3 is an SQL database engine in a C library. Programs that link the SQLite3 library can have SQL database access without running a separate RDBMS process. | |
| squat | ||
| sratoolkit | The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format. | |
| srilm | ||
| ssh | ||
| stacks | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. | |
| staden-io-lib | Io_lib is a library for reading/writing various bioinformatics file formats. | |
| stampy | ||
| star | star | STAR is an ultrafast universal RNA-seq aligner. |
| stells2 | ||
| strelka | ||
| stringtie | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. | |
| structure | ||
| subread | ||
| subversion | Apache Subversion - an open source version control system. | |
| suite-sparse | SuiteSparse is a suite of sparse matrix algorithms | |
| superfamily | ||
| superfold | ||
| superlu-dist | A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. | |
| superlu | SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. SuperLU is designed for sequential machines. | |
| supernova | ||
| survivor | ||
| svn | ||
| swarm | ||
| swig | SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl. It works by taking the declarations found in C/C++ header files and using them to generate the wrapper code that scripting languages need to access the underlying C/C++ code. In addition, SWIG provides a variety of customization features that let you tailor the wrapping process to suit your application. | |
| symos97 | ||
| sz | Error-bounded Lossy Compressor for HPC Data |
T
| module name | link to docs | description |
|---|---|---|
| tabix | Generic indexer for TAB-delimited genome position files | |
| tablet | ||
| tar | GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation. | |
| targetp | ||
| tassel | ||
| tcl | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Open source and business-friendly, Tcl is a mature yet evolving language that is truly cross platform, easily deployed and highly extensible. | |
| tcltk | ||
| tcsh | Tcsh is an enhanced but completely compatible version of csh, the C shell. Tcsh is a command language interpreter which can be used both as an interactive login shell and as a shell script command processor. Tcsh includes a command line editor, programmable word completion, spelling correction, a history mechanism, job control and a C language like syntax. | |
| teckit | TECkit is a low-level toolkit intended to be used by applications for conversions between text encodings. For example, it can be used when importing legacy text into a Unicode-based application. | |
| telseq | ||
| tensorflow | ||
| tepid | ||
| termcap | This is the GNU termcap library, a library of C functions that enable programs to send control strings to terminals in a way independent of the terminal type. | |
| tesseract | ||
| texinfo | Texinfo is the official documentation format of the GNU project. | |
| texlive | TeX Live is an easy (we hope) way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world. | |
| tgicl | ||
| thrift | Software framework for scalable cross-language services development. | |
| tiff | ||
| tinker | tinker | |
| tinker9 | ||
| tix | Tix is a powerful high-level widget set that expands the capabilities of your Tk/Tcl and Python applications. | |
| tk | Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, and can produce rich, native applications that run unchanged across Windows, Mac OS X, Linux and more. | |
| tmolex | tmolex | |
| tophat | Spliced read mapper for RNA-Seq. | |
| torch | ||
| torque | ||
| totalview | ||
| transcode | ||
| transdecoder | ||
| transfuse | ||
| transrate | ||
| treemix | ||
| treepl | ||
| trf | Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. | |
| trim_galore | ||
| trimal | ||
| trimmomatic | trimmomatic | A flexible read trimming tool for Illumina NGS data. |
| trinity | Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. | |
| trinotate | Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms | |
| trycycler | ||
| turbomole | turbomole |
U
| module name | link to docs | description |
|---|---|---|
| uchardet | uchardet is an encoding detector library, which takes a sequence of bytes in an unknown character encoding without any additional information, and attempts to determine the encoding of the text. Returned encoding names are iconv-compatible. | |
| ucx | a communication library implementing high-performance messaging for MPI/PGAS frameworks | |
| udunits | Automated units conversion | |
| ugene | ||
| umi_varcal | ||
| unicycler | ||
| unixodbc | ODBC is an open specification for providing application developers with a predictable API with which to access Data Sources. Data Sources include SQL Servers and any Data Source with an ODBC Driver. | |
| unrar | RAR archive extraction utility | |
| unuran | Universal Non-Uniform Random number generator. | |
| unzip | Unzip is a compression and file packaging/archive utility. | |
| uppasd | ||
| uriparser | uriparser is a strictly RFC 3986 compliant URI parsing and handling library written in C89 (ANSI C). | |
| uspex | ||
| utf8cpp | A simple, portable and lightweight generic library for handling UTF-8 encoded strings. | |
| utf8proc | A clean C library for processing UTF-8 Unicode data: normalization, case-folding, graphemes, and more | |
| util-linux-uuid | Util-linux is a suite of essential utilities for any Linux system. | |
| util-macros | This is a set of autoconf macros used by the configure.ac scripts in other Xorg modular packages, and is needed to generate new versions of their configure scripts with autoconf. |
V
| module name | link to docs | description |
|---|---|---|
| vasp | vasp | |
| vasp46 | ||
| vasp52 | ||
| vasp53 | ||
| vaspkit | ||
| vc | SIMD Vector Classes for C++ | |
| vcftools | ||
| vdt | Vectorised math. A collection of fast and inline implementations of mathematical functions. | |
| veccore | SIMD Vectorization Library for VecGeom and GeantV. | |
| vecgeom | The vectorized geometry library for particle-detector simulation (toolkits). | |
| velvet | velvet | |
| velvetopt | ||
| vesta | ||
| videoproto | X Video Extension. | |
| viennarna | ||
| vina | ||
| vips | ||
| virtest | Header-only unit test framework, as easy as possible to use | |
| visit | ||
| vmd | vmd | |
| voropp | Voro++ is a open source software library for the computation of the Voronoi diagram, a widely-used tessellation that has applications in many scientific fields. | |
| vpssolution | ||
| vsearch | VSEARCH is a versatile open-source tool for metagenomics. | |
| vtk | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. |
W
| module name | link to docs | description |
|---|---|---|
| wannier90 | Wannier90 calculates maximally-localised Wannier functions (MLWFs). | |
| wengan | ||
| wengan_gunzipped | ||
| wget | GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. | |
| wgs | ||
| which | GNU which - is a utility that is used to find which executable (or alias or shell function) is executed when entered on the shell prompt. | |
| whiteboxtools | ||
| wien2k | wien2k | |
| wigtobigwig | ||
| wine | ||
| wise | ||
| wtdbg | ||
| wxpython | ||
| wxwidgets | wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platforms native API rather than emulating the GUI. Its also extensive, free, open-source and mature. |
X
| module name | link to docs | description |
|---|---|---|
| x264 | Software library and application for encoding video streams | |
| xcb-proto | xcb-proto provides the XML-XCB protocol descriptions that libxcb uses to generate the majority of its code and API. | |
| xcb-util-image | The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib. | |
| xcb-util-keysyms | The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib. | |
| xcb-util-renderutil | The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib. | |
| xcb-util-wm | The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib. | |
| xcb-util | The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. These experimental libraries provide convenience functions and interfaces which make the raw X protocol more usable. Some of the libraries also provide client-side code which is not strictly part of the X protocol but which have traditionally been provided by Xlib. | |
| xclip | xclip is a command line utility that is designed to run on any system with an X11 implementation. It provides an interface to X selections (the clipboard) from the command line. It can read data from standard in or a file and place it in an X selection for pasting into other X applications. xclip can also print an X selection to standard out, which can then be redirected to a file or another program. | |
| xcrysden | ||
| xerces-c | Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. | |
| xextproto | X Protocol Extensions. | |
| xf86vidmodeproto | XFree86 Video Mode Extension. | |
| xfce | ||
| xineramaproto | X Xinerama Extension. | |
| xkbcomp | The X Keyboard (XKB) Extension essentially replaces the core protocol definition of a keyboard. The extension makes it possible to specify clearly and explicitly most aspects of keyboard behaviour on a per-key basis, and to track more closely the logical and physical state of a keyboard. It also includes a number of keyboard controls designed to make keyboards more accessible to people with physical impairments. | |
| xkbdata | The XKB data files for the various keyboard models, layouts, and locales. | |
| xmgrace | ||
| xmipp | ||
| xorg-cf-files | The xorg-cf-files package contains the data files for the imake utility, defining the known settings for a wide variety of platforms (many of which have not been verified or tested in over a decade), and for many of the libraries formerly delivered in the X.Org monolithic releases. | |
| xproto | X Window System Core Protocol. | |
| xrandr | xrandr - primitive command line interface to X11 Resize, Rotate, and Reflect (RandR) extension. | |
| xsimd | C++ wrappers for SIMD intrinsics | |
| xtb | ||
| xtensor | Multi-dimensional arrays with broadcasting and lazy computing | |
| xterm | The xterm program is a terminal emulator for the X Window System. It provides DEC VT102 and Tektronix 4014 compatible terminals for programs that cant use the window system directly. | |
| xtl | QuantStack tools library | |
| xtrans | xtrans is a library of code that is shared among various X packages to handle network protocol transport in a modular fashion, allowing a single place to add new transport types. It is used by the X server, libX11, libICE, the X font server, and related components. | |
| xxdiff | ||
| xxhash | xxHash is an Extremely fast Hash algorithm, running at RAM speed limits. It successfully completes the SMHasher test suite which evaluates collision, dispersion and randomness qualities of hash functions. Code is highly portable, and hashes are identical on all platforms (little / big endian). | |
| xz | XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils. |
Y
| module name | link to docs | description |
|---|---|---|
| yaha | ||
| yasm | Yasm is a complete rewrite of the NASM-2.11.06 assembler. It supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes and outputs binary, ELF32 and ELF64 object formats. |
Z
| module name | link to docs | description |
|---|---|---|
| z3 | Z3 is a theorem prover from Microsoft Research. It is licensed under the MIT license. | |
| zfp | zfp is an open source C/C++ library for high-fidelity, high-throughput lossy compression of floating-point and integer multi-dimensional arrays. | |
| zip | Zip is a compression and file packaging/archive utility. | |
| zlib | A free, general-purpose, legally unencumbered lossless data-compression library. | |
| zoltan | The Zoltan library is a toolkit of parallel combinatorial algorithms for parallel, unstructured, and/or adaptive scientific applications. Zoltans largest component is a suite of dynamic load-balancing and partitioning algorithms that increase applications parallel performance by reducing idle time. Zoltan also has graph coloring and graph ordering algorithms, which are useful in task schedulers and parallel preconditioners. | |
| zstd | Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios. | |
| zziplib | The zziplib provides read access to zipped files in a zip-archive, using compression based solely on free algorithms provided by zlib. It also provides a functionality to overlay the archive filesystem with the filesystem of the operating system environment. |
Last update Mon Jun 1 08:06:40 AM CEST 2026
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