| R |
lang |
R is a free software environment for statistical computing and graphics. |
| abinit |
chem |
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. |
| afni |
bio |
AFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of anatomical and functional MRI (FMRI) data. It is freely available (both in source code and in precompiled binaries) for research purposes. The software is made to run on virtually an Unix system with X11 and Motif displays. Binary Packages are provided for MacOS and Linux systems including Fedora, Ubuntu (including Ubuntu under the Windows Subsytem for Linux) |
| agrep |
tools |
AGREP - approximate GREP for fast fuzzy string searching. Files are searched for a string or regular expression, with approximate matching capabilities and user-definable records. |
| alamode |
chem |
ALAMODE is designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids.
By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and
anharmonic force constants straightforwardly with ALAMODE. Using the anharmonic force constants,
you can also calculate lattice thermal conductivity from first principles.
|
| alphafold |
bio |
Open source code for AlphaFold
|
| amber |
bio |
A suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community. |
| amptorch |
data |
AMPtorch is a PyTorch implementation of the Atomistic Machine-learning Package (AMP) code that seeks to provide users with improved performance and flexibility as compared to the original code. The implementation does so by benefiting from state-of-the-art machine learning methods and techniques to be optimized in conjunction with high-throughput supercomputers. AMPtorch is built on top of PyTorch Geometric and Skorch.
|
| anaconda |
lang |
Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
|
| angsd |
bio |
Program for analysing NGS data. |
| ansys |
cae |
ANSYS simulation software enables organizations to confidently predict
how their products will operate in the real world. We believe that every product is
a promise of something greater. |
| ant |
devel |
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. The main known usage of Ant is the build of
Java applications. |
| ants |
data |
ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing,
interpreting and visualizing multidimensional data. |
| anvio |
data |
Anvi'o is an open-source, community-driven analysis and visualization platform for microbial 'omics. It brings together many aspects of today's cutting-edge strategies including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.
|
| apr |
tools |
The mission of the Apache Portable Runtime (APR) project is to create and maintain software libraries that provide a predictable and consistent interface to underlying platform-specific implementations. |
| apr-util |
tools |
The mission of the Apache Portable Runtime (APR) project is to create and maintain software libraries that provide a predictable and consistent interface to underlying platform-specific implementations. |
| archspec |
%!s(<nil>) |
A library for detecting, labeling, and reasoning about microarchitectures |
| aria2 |
compiler |
aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. |
| armadillo |
numlib |
Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
as well as a subset of trigonometric and statistics functions. |
| arpack-ng |
numlib |
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
| ase |
chem |
The Atomic Simulation Environment (ASE) is a set of tools and Python modules for
setting up, manipulating, running, visualizing and analyzing atomistic simulations.
|
| aspera-connect |
tools |
Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and
downloads with an Aspera transfer server. |
| atat |
chem |
The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools
|
| atk |
vis |
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.
|
| atom |
tools |
Atom is a hackable text editor for the 21st century, built on Electron, and based on everything we love about our favorite editors. |
| augustus |
bio |
AUGUSTUS is a program to find genes and their structures in one or more genomes. |
| automake |
devel |
Automake: GNU Standards-compliant Makefile generator |
| autotools |
devel |
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool |
| awscli |
tools |
This package provides a unified command line interface to Amazon Web Services.
|
| bamtools |
bio |
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| bart |
bio |
BART (Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcription factors (TFs) that bind at genomic cis-regulatory regions to regulate gene expression in the human or mouse genomes, given a query gene set or a ChIP-seq dataset as input. |
| bart-mri |
bio |
The Berkeley Advanced Reconstruction Toolbox (BART) toolbox is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging developed by the research groups of Martin Uecker (Goettingen University), Jon Tamir (UT Austin), and Michael Lustig (UC Berkeley). It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. The command-line tools provide direct access to basic operations on multi-dimensional arrays as well as efficient implementations of many calibration and reconstruction algorithms for parallel imaging and compressed sen.
|
| bazel |
%!s(<nil>) |
Bazel is a build tool that builds code quickly and reliably.
It is used to build the majority of Google's software. |
| bbmap |
bio |
BBMap includes a short read aligner, and other bioinformatic tools. |
| bcftools |
bio |
SAMtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence
variants |
| bcl2fastq2 |
bio |
bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
Illumina sequencing systems to standard FASTQ file formats for downstream analysis. |
| beagle |
bio |
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. |
| bedops |
bio |
BEDOPS is an open-source command-line toolkit that performs highly efficient and
scalable Boolean and other set operations, statistical calculations, archiving, conversion and
other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for
distributing whole-genome analyses across a computational cluster. |
| bedtools |
bio |
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps
and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF,
and SAM/BAM. |
| berkeley_db |
tools |
Berkeley DB is a family of embedded key-value database libraries providing scalable high-performance data management services to applications. |
| berkeleygw |
phys |
The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle
properties and the optical responses of a large variety of materials from bulk periodic crystals to
nanostructures such as slabs, wires and molecules. |
| bicseq2-norm |
bio |
BICseq2 is an algorithm developed for the normalization of high-throughput sequencing (HTS) data and detect copy number variations (CNV) in the genome. BICseq2 can be used for detecting CNVs with or without a control genome. BICseq2-norm is for normalizing potential biases in the sequencing data. |
| bicseq2-seg |
bio |
BICseq2 is an algorithm developed for the normalization of high-throughput sequencing (HTS) data and detect copy number variations (CNV) in the genome. BICseq2 can be used for detecting CNVs with or without a control genome. BICseq2-seg is for detecting CNVs based on the normalized data given by BICseq2-norm. |
| bioawk |
bio |
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk. |
| bioconda |
bio |
Bioconda is a channel for the conda package manager specializing in bioinformatics software. |
| bioperl |
bio |
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. |
| biopython |
bio |
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in
bioinformatics. |
| bismark |
bio |
A tool to map bisulfite converted sequence reads and
determine cytosine methylation states |
| bison |
lang |
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 |
%!s(<nil>) |
Variation graphs provide a succinct encoding of the sequences of many genomes. |
| blast |
bio |
Basic Local Alignment Search Tool, or BLAST, is an algorithm
for comparing primary biological sequence information, such as the amino-acid
sequences of different proteins or the nucleotides of DNA sequences. |
| blat |
bio |
BLAT on DNA is designed to quickly find sequences of 95% and
greater similarity of length 25 bases or more. |
| blender |
vis |
Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline,
modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video
editing and game creation.
|
| blitz++ |
lib |
Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++
with a speed comparable to Fortran implementations, while preserving an object-oriented interface |
| boost |
%!s(<nil>) |
Boost provides free peer-reviewed portable C++ source libraries. |
| bowtie2 |
bio |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s
of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,
its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. |
| bsmap |
bio |
BSMAP is a short reads mapping program for bisulfite sequencing in DNA methylation study. Bisulfite treatment coupled with next generation sequencing could estimate the methylation ratio of every single Cytosine location in the genome by mapping high throughput bisulfite reads to the reference sequences. |
| bwa |
bio |
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
relatively short nucleotide sequences against a long reference sequence such as the human genome. |
| bzip2 |
tools |
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. |
| caffe2 |
lib |
Caffe is a deep learning framework made with expression, speed, and modularity in mind |
| cairo |
vis |
Cairo is a 2D graphics library with support for multiple output devices.
Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,
PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB |
| canu |
bio |
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing |
| caviar |
bio |
caviar is a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants. |
| cc3d |
vis |
CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D's intuitive interface makes Virtual Tissue modeling accessible to users without extensive software development or programming experience.
|
| cd-hit |
bio |
CD-HIT is a very widely used program for clustering and
comparing protein or nucleotide sequences. |
| cellassign |
bio |
cellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows.
|
| cellprofiler |
bio |
CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
|
| cellranger |
%!s(<nil>) |
A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting. |
| cellranger-arc |
%!s(<nil>) |
Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. |
| cellranger-atac |
bio |
Cell Ranger ATAC is a set of analysis pipelines that process
Chromium Single Cell ATAC data. |
| cellranger-dna |
bio |
Cell Ranger DNA is a set of analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation (CNV), and compare heterogeneity among cells. |
| cesm |
geo |
CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. |
| cgal |
numlib |
The goal of the CGAL Open Source Project is to provide easy access to efficient
and reliable geometric algorithms in the form of a C++ library. |
| chemps2 |
chem |
CheMPS2 is a scientific library which contains a spin-adapted implementation of the
density matrix renormalization group (DMRG) for ab initio quantum chemistry. |
| circos |
bio |
Circos is a software package for visualizing data and information.
It visualizes data in a circular layout - this makes Circos ideal for exploring
relationships between objects or positions. |
| clang |
%!s(<nil>) |
C, C++, Objective-C compiler, based on LLVM. Does not
include C++ standard library -- use libstdc++ from GCC. |
| clanggcc |
%!s(<nil>) |
Clang based compiler toolchain |
| clapack |
math |
C version of LAPACK |
| clara-parabricks |
bio |
NVIDIA Parabricks is the only GPU-accelerated computational genomics toolkit that delivers fast and accurate analysis for sequencing centers, clinical teams, genomics researchers, and next-generation sequencing instrument developers.
|
| clearcut |
bio |
Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. |
| clhep |
numlib |
The CLHEP project is intended to be a set of HEP-specific foundation and
utility classes such as random generators, physics vectors, geometry and linear algebra.
CLHEP is structured in a set of packages independent of any external package. |
| clibs |
lib |
Provides base libs/headers needed to build various other things on the kernel
Maintained by the ITS-RCI team. |
| cloudcompare |
vis |
CloudCompare is a 3D point cloud (and triangular mesh) processing software. It has been originally designed to perform comparison between two dense 3D points clouds (such as the ones acquired with a laser scanner) or between a point cloud and a triangular mesh. |
| cmake |
devel |
CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software. |
| cnnpeaks |
bio |
CNN-peaks is a Convolution Neural Network(CNN) based ChIP-Seq peak calling software.
|
| code-server |
tools |
Run VS Code on any machine anywhere and access it in the browser.
|
| codeblocks |
lang |
Code::Blocks is a free C, C++ and Fortran IDE built to meet the most demanding needs of its users. It is designed to be very extensible and fully configurable. |
| cp-analyst |
bio |
CellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CellProfiler is an image processing package to generate morphometric measurements. |
| cp2k |
chem |
CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular
simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different
methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and
classical pair and many-body potentials. |
| cppcheck |
tools |
Cppcheck is a static analysis tool for C/C++ code. It provides unique code analysis to detect bugs and focuses on detecting undefined behaviour
and dangerous coding constructs. |
| cromwell |
tools |
Cromwell is a Workflow Management System geared towards scientific workflows. |
| crossftp |
tools |
CrossFTP is a free FTP, SFTP, WebDav, Amazon S3, Amazon Glacier, Microsoft Azure, Google storage, and OpenStack Swift client for Win, Mac, and Linux. |
| cuda |
system |
CUDA (formerly Compute Unified Device Architecture) is a parallel
computing platform and programming model created by NVIDIA and implemented by the
graphics processing units (GPUs) that they produce. CUDA gives developers access
to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. |
| cudatoolkit |
tools |
The NVIDIA CUDA Toolkit provides a development environment for creating high performance GPU-accelerated
applications. With the CUDA Toolkit, you can develop, optimize and deploy your applications on GPU-
accelerated embedded systems, desktop workstations, enterprise data centers, cloud-based platforms and HPC
supercomputers. The toolkit includes GPU-accelerated libraries, debugging and optimization tools, a C/C++
compiler and a runtime library to deploy your application.
|
| cudnn |
numlib |
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. |
| cufflinks |
bio |
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. |
| cumulus_feature_barcoding |
bio |
A fast C++ tool to extract feature-count matrix from sequence reads in FASTQ files. We uses isal-l for decompressing and Heng Li's kseq library for read parsing. It is used by Cumulus for feature-count matrix generation of cell hashing, nucleus hashing, CITE-Seq and Perturb-seq protocols, using either 10x Genomics V2 or V3 chemistry.
|
| curl |
tools |
libcurl is a free and easy-to-use client-side URL transfer library,
supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP,
LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP.
libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP
form based upload, proxies, cookies, user+password authentication (Basic,
Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling
and more.
|
| cutadapt |
bio |
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. |
| cytoscape |
tools |
Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. |
| danpos |
bio |
A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2. |
| dbg2olc |
%!s(<nil>) |
A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads. |
| ddd |
vis |
DDD is a graphical front-end for command-line debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger bashdb, the GNU Make debugger remake, or the Python debugger pydb. |
| decontaminer |
bio |
decontaMiner, a tool for detecting contaminating organisms in human unmapped sequences. |
| deeplabcut |
bio |
DeepLabCut is a toolbox for markerless pose estimation of animals performing various tasks.
|
| deeptools |
%!s(<nil>) |
deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome. |
| diamond |
%!s(<nil>) |
DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. |
| doxygen |
devel |
Doxygen is a documentation system for C++, C, Java, Objective-C, Python,
IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
| dragonn |
data |
The dragonn package implements Deep RegulAtory GenOmic Neural Networks (DragoNNs) for predictive modeling of regulatory genomics, nucleotide-resolution feature discovery, and simulations for systematic development and benchmarking.
|
| drmaa |
tools |
DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed
Resource Management Application API (DRMAA) version 1 for submission and control of jobs to
Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same
high-level API to link their software with different cluster/resource management systems.
|
| eccodes |
tools |
ecCodes is a package developed by ECMWF which provides an application programming interface and
a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2,
WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). |
| eclipse |
bio |
Eclipse provides IDEs and platforms for many programming languages. This module includes Java support. |
| eigen |
math |
Eigen is a C++ template library for linear algebra:
matrices, vectors, numerical solvers, and related algorithms. |
| eigensoft |
bio |
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al.
2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal
components analysis to explicitly model ancestry differences between cases and controls along continuous axes of
variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral
populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT
package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. |
| elpa |
%!s(<nil>) |
Eigenvalue SoLvers for Petaflop-Applications . |
| emboss |
bio |
EMBOSS is 'The European Molecular Biology Open Software Suite'.
EMBOSS is a free Open Source software analysis package specially developed for
the needs of the molecular biology (e.g. EMBnet) user community. |
| epacts |
tools |
EPACTS (Efficient and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers. |
| epic |
bio |
epic is a software package for finding medium to diffusely enriched domains in chip-seq data. It is a fast, parallel and memory-efficient implementation of the popular SICER algorithm. |
| epstopdf |
tools |
Epstopdf is a Perl script that converts an EPS file to an ‘encapsulated’ PDF file (a single page file whose media box is the same as the original EPS’s bounding box). |
| esmf |
geo |
The Earth System Modeling Framework (ESMF) is software for building and coupling weather,
climate, and related models. |
| evm |
bio |
The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. |
| exonerate |
bio |
Exonerate is a generic tool for pairwise sequence comparison.
It allows you to align sequences using a many alignment models, using either
exhaustive dynamic programming, or a variety of heuristics. |
| fasta |
bio |
The FASTA programs find regions of local or global (new) similarity between
protein or DNA sequences, either by searching Protein or DNA databases, or by identifying
local duplications within a sequence. |
| fastenloc |
bio |
fastENLOC: fast enrichment estimation aided colocalization analysis enables integrative genetic association analysis of molecular QTL data and GWAS data. |
| fastqc |
bio |
FastQC is a Java application which takes a FastQ file and runs a series
of tests on it to generate a comprehensive QC report. |
| fastqtl |
bio |
FastQTL is a QTL mapper |
| fastx-toolkit |
bio |
The FASTX-Toolkit is a collection of command line tools for
Short-Reads FASTA/FASTQ files preprocessing. |
| febio |
cae |
FEBio is a nonlinear finite element solver that is specifically designed for biomechanics and biophysics applications. |
| ffmpeg |
vis |
A complete, cross-platform solution to record, convert and stream audio and video. |
| fftw |
%!s(<nil>) |
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. |
| fgsl |
numlib |
FGSL: A Fortran interface to the GNU Scientific Library |
| fgwas |
lib |
fgwas is a command line tool for integrating functional genomic information into a genome-wide association study (GWAS). |
| fiji |
tools |
Fiji is an image processing distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. |
| finestructure |
bio |
fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using
dense sequencing data. |
| fltk |
vis |
FLTK 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. |
| fmriprep |
bio |
fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI). |
| fortrangis |
geo |
FortranGIS project includes a collection of Fortran interfaces to some common Open Source GIS (Geographic Information System) software libraries, plus some more Fortran-specific tools. |
| freebayes |
bio |
FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. |
| freesurfer |
bio |
FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data.
FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. |
| freexl |
lib |
FreeXL is an open source library to extract valid data from within an
Excel (.xls) spreadsheet.
|
| fribidi |
lang |
The Free Implementation of the Unicode Bidirectional Algorithm. |
| fsa |
bio |
FSA:Fast Statistical Alignment, is a probabilistic multiple sequence alignment algorithm which uses a distance-based approach to aligning homologous protein, RNA or DNA sequences. |
| fsl |
bio |
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
| funannotate |
bio |
Funannotate is a genome prediction, annotation, and comparison software package. It was originally
written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to
accomodate larger genomes. The impetus for this software package was to be able to accurately and
easily annotate a genome for submission to NCBI GenBank. Existing tools (such as Maker) require
significant manually editing to comply with GenBank submission rules, thus funannotate is aimed at
simplifying the genome submission process. |
| gatk |
bio |
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
with a primary focus on variant discovery and genotyping as well as strong emphasis on
data quality assurance. Its robust architecture, powerful processing engine and
high-performance computing features make it capable of taking on projects of any size. |
| gaussian |
chem |
Gaussian is a suite of electronic-structure codes. |
| gawk |
tools |
The awk utility interprets a special-purpose programming language that makes it possible to handle
simple data-reformatting jobs with just a few lines of code. |
| gcc |
compiler |
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
as well as libraries for these languages (libstdc++, libgcj,...). |
| gcccuda |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. |
| gcloud-sdk |
tools |
The Cloud SDK is a set of tools for Cloud Platform. It contains gcloud, gsutil, and bq, which you can use to access Google Compute Engine, Google Cloud Storage, Google BigQuery, and other products and services from the command-line. |
| gd |
bio |
GD.pm - Interface to Gd Graphics Library |
| gdal |
data |
GDAL is a translator library for raster 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 abstract data model
to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
data translation and processing. |
| gdal-grass |
data |
The idea of the GDAL-GRASS plugin is to directly access GRASS raster and vector data from outside. Any GDAL enabled software (QGIS, R, ...) can read and write through the plugin from the GRASS database. |
| gdb |
debugger |
The GNU Project Debugger |
| gdc-client |
tools |
The gdc-client provides several convenience functions over
the GDC API which provides general download/upload via HTTPS. |
| gdrcopy |
%!s(<nil>) |
A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. |
| geany |
tools |
Geany is a text editor using the GTK+ toolkit with basic features of an integrated development environment. |
| gemma |
bio |
Genome-wide Efficient Mixed Model Association |
| genometools |
bio |
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules. |
| genrich |
bio |
Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment. |
| geos |
math |
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
| gffcompare |
bio |
The program gffcompare can be used to compare, merge, annotate, and estimate accuracy of one or more GFF files (the 'query' files), when compared with a reference annotation (also provided as GFF). |
| gftp |
tools |
gFTP is a free multithreaded file transfer client for *NIX based machines. |
| ghostscript |
tools |
Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to
different targets. It used to be part of the cups printing stack, but is no longer used for that. |
| git |
tools |
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. |
| git-lfs |
tools |
Git Large File Storage (LFS) replaces large files such as audio
samples, videos, datasets, and graphics with text pointers inside Git, while
storing the file contents on a remote server like GitHub.com |
| glade |
vis |
Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit
and the GNOME desktop environment. |
| glew |
lib |
The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. |
| glfw |
lib |
GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop.
It provides a simple API for creating windows, contexts and surfaces, receiving input and events.
|
| glib |
vis |
GLib is one of the base libraries of the GTK+ project |
| globus_cli |
tools |
Globus CLI is a standalone application that can be installed on the user’s machine and used to access the Globus file transfer service. |
| gmap-gsnap |
bio |
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
GSNAP: Genomic Short-read Nucleotide Alignment Program |
| gmp |
math |
GMP is a free library for arbitrary precision arithmetic,
operating on signed integers, rational numbers, and floating point numbers. |
| gnupg |
tools |
GnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880 (also known as PGP). GnuPG allows you to encrypt and sign your data and communications; it features a versatile key management system, along with access modules for all kinds of public key directories. |
| gnuplot |
vis |
Portable interactive, function plotting utility |
| go |
lang |
Go is an open source programming language that makes it easy to build
simple, reliable, and efficient software. |
| gobject-introspection |
devel |
GObject introspection is a middleware layer between C libraries
(using GObject) and language bindings. The C library can be scanned at
compile time and generate a metadata file, in addition to the actual
native C library. Then at runtime, language bindings can read this
metadata and automatically provide bindings to call into the C library. |
| goffice |
lib |
GOffice is a GObject based C library. It provides easy API access to creating and manipulating graphs and canvases. |
| gompi |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain,
including OpenMPI for MPI support. |
| gompic |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit,
including OpenMPI for MPI support with CUDA features enabled. |
| google-api |
tools |
Google APIs give you programmatic access to Google Maps, Google Drive, YouTube, and many other Google products. |
| goolf |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain, including
OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
| goolfc |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit,
including OpenMPI for MPI support with CUDA features enabled, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK with CUDA features enabled. |
| gperf |
base |
None |
| gperftools |
tools |
gperftools are for use by developers so that they can create more robust applications.
Especially of use to those developing multi-threaded applications in C++ with templates.
Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. |
| gpumd |
chem |
GPUMD stands for Graphics Processing Units Molecular Dynamics. It is a general-purpose molecular dynamics (MD) code fully implemented on graphics processing units (GPUs). |
| gpunufft |
data |
GPU Regridding of arbitrary 3-D/2-D MRI data |
| gpustat |
tools |
dstat-like utilization monitor for NVIDIA GPUs |
| grace |
vis |
Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. |
| grass |
geo |
The Geographic Resources Analysis Support System - used
for geospatial data management and analysis, image processing,
graphics and maps production, spatial modeling, and visualization |
| grib_api |
data |
The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python
programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of
command line tools is also provided to give quick access to GRIB messages. |
| gromacs |
chem |
GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
| gsl |
numlib |
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
The library provides a wide range of mathematical routines such as random number generators, special functions
and least-squares fitting. |
| gtk+ |
vis |
The GTK+ 3 package contains libraries used for creating graphical user interfaces for applications.
|
| gurobi |
math |
The Gurobi Optimizer is a state-of-the-art solver for mathematical programming.
The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern
architectures and multi-core processors, using the most advanced implementations of the
latest algorithms. |
| gzip |
tools |
gzip (GNU zip) is a popular data compression program as a replacement for compress |
| hapflow |
bio |
HapFlow is a python application for visualising haplotypes present in sequencing data. It identifies variant profiles present and reads and creates an abstract visual representation of these profiles to make haplotypes easier to identify. |
| hdf |
data |
HDF (also known as HDF4) is a library and multi-object file format for storing and managing data
between machines. |
| hdf-eos |
data |
The HDF-EOS2 is a software library designed built on HDF4* to support EOS-specific data structures, namely Grid, Point, and Swath. |
| hdf5 |
%!s(<nil>) |
HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
| hexrd |
phys |
HEXRD provides a collection of resources for analysis of x-ray diffraction data, especially high-energy x-ray diffraction. HEXRD is comprised of a library and API for writing scripts, a command line interface, and an interactive graphical user interface. |
| hic-pro |
bio |
HiC-Pro is an optimized and flexible pipeline for Hi-C data processing. |
| hisat2 |
bio |
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads
(both DNA and RNA) against the general human population (as well as against a single reference genome). |
| homer |
tools |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data. |
| hoomd |
chem |
HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. |
| htslib |
bio |
A C library for reading/writing high-throughput sequencing data.
This package includes the utilities bgzip and tabix |
| hunspell |
chem |
Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding. Hunspell interfaces: Ispell-like terminal interface using Curses library, Ispell pipe interface, C++ class and C functions. |
| hwloc |
%!s(<nil>) |
The Portable Hardware Locality (hwloc) software package provides a portable
abstraction (across OS, versions, architectures, ...) of the hierarchical
topology of modern architectures, including NUMA memory nodes, sockets, shared
caches, cores and simultaneous multithreading. It also gathers various system
attributes such as cache and memory information as well as the locality of I/O
devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily
aims at helping applications with gathering information about modern computing
hardware so as to exploit it accordingly and efficiently.
|
| hydrator |
data |
Hydrator converts Twitter IDs into JSON files. |
| hypre |
numlib |
Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers.
The problems of interest arise in the simulation codes being developed at LLNL and elsewhere
to study physical phenomena in the defense, environmental, energy, and biological sciences. |
| icu |
lib |
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization
support for software applications. |
| idl |
%!s(<nil>) |
IDL is an interpreted programming language used to create analyses and visualizations of numerical data. |
| idr |
bio |
The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. The IDR method compares a pair of ranked lists of identifications (such as ChIP-seq peaks). |
| igvtools |
bio |
This package contains command line utilities for preprocessing,
computing feature count density (coverage), sorting, and indexing data files.
See also http://www.broadinstitute.org/software/igv/igvtools_commandline. |
| iimpi |
%!s(<nil>) |
Intel C/C++ and Fortran compilers, alongside Intel MPI. |
| iintelmpi |
toolchain |
Intel C/C++ and Fortran compilers with IntelMPI. |
| imagemagick |
vis |
ImageMagick is a software suite to create, edit, compose, or convert bitmap images |
| imkl |
%!s(<nil>) |
Intel oneAPI Math Kernel Library |
| imkl-fftw |
%!s(<nil>) |
FFTW interfaces using Intel oneAPI Math Kernel Library |
| impi |
%!s(<nil>) |
Intel MPI Library, compatible with MPICH ABI |
| impute2 |
bio |
IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation
and haplotype phasing program based on ideas from Howie et al. 2009 |
| inkscape |
lib |
Inkscape is a free and open source professional vector graphics editor. |
| intel |
%!s(<nil>) |
Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). |
| intel-compilers |
compiler |
Intel C, C++ & Fortran compilers (classic and oneAPI) |
| intelmpi |
mpi |
IntelMPI from Intel. |
| intervene |
bio |
Intervene is a tool for intersection and visualization of multiple genomic region sets. |
| intltool |
lang |
The Intltool is an internationalization tool used for extracting translatable strings from source files, collecting the extracted strings with messages from traditional source files, and merging the translations into .xml, .desktop and .oaf files. |
| io_lib |
bio |
Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. |
| iqtree |
bio |
Efficient phylogenomic software by maximum likelihood |
| irfinder |
bio |
IRFinder is a tool for detecting intron retention from RNA-Seq experiments. |
| isaacgym |
data |
NVIDIA’s physics simulation environment for reinforcement learning research.
|
| isoseqenv |
bio |
IsoDeq3 is a Scalable De Novo Isoform Discovery |
| jags |
math |
JAGS is Just Another Gibbs Sampler. It is a program for analysis
of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation |
| jasper |
vis |
The JasPer Project is an open-source initiative to provide a free
software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. |
| java |
lang |
Java Platform, Standard Edition (Java SE) lets you develop and deploy
Java applications on desktops and servers. |
| jcuda |
bio |
Java bindings for NVIDIA CUDA and related libraries. |
| jellyfish |
%!s(<nil>) |
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. |
| jq |
tools |
jq is a lightweight and flexible command-line JSON processor. |
| jtreeview |
vis |
TreeView is an open-source Java app for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it (or parts of it) into a figure. |
| juicer |
bio |
Juicer is a one-click pipeline for processing terabase scale Hi-C datasets. |
| julia |
lang |
Julia is a high-level, high-performance dynamic programming language for numerical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. |
| junit |
devel |
A programmer-oriented testing framework for Java. |
| jupyter_conda |
lang |
Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
|
| kallisto |
bio |
Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. |
| kim-api |
chem |
Open Knowledgebase of Interatomic Models.
KIM is an API and OpenKIM is a collection of interatomic models (potentials) for
atomistic simulations. This is a library that can be used by simulation programs
to get access to the models in the OpenKIM database.
This EasyBuild only installs the API, the models can be installed with the
package openkim-models, or the user can install them manually by running
kim-api-collections-management install user MODELNAME
or
kim-api-collections-management install user OpenKIM
to install them all.
|
| knime |
data |
KNIME is an analytics platform for data mining. |
| kraken |
bio |
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. |
| kraken2 |
bio |
Kraken is a system for assigning taxonomic labels to short DNA sequences,
usually obtained through metagenomic studies. Previous attempts by other
bioinformatics software to accomplish this task have often used sequence
alignment or machine learning techniques that were quite slow, leading to
the development of less sensitive but much faster abundance estimation
programs. Kraken aims to achieve high sensitivity and high speed by
utilizing exact alignments of k-mers and a novel classification algorithm. |
| kubectl |
tools |
The Kubernetes command-line tool, kubectl, allows you to run commands against Kubernetes clusters. You can use kubectl to deploy applications, inspect and manage cluster resources, and view logs. |
| lame |
data |
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. |
| lammps |
chem |
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. |
| lapack |
numlib |
LAPACK is written in Fortran90 and provides routines for solving systems of
simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue
problems, and singular value problems. |
| leda |
lib |
RStudio is a set of integrated tools designed to help you be more productive with R. LEDA is a C++ class library for efficient data types and algorithms that provide algorithmic in-depth knowledge of graph- and network problems, geometric computations, combinatorial opimization and other. |
| leptonica |
vis |
Leptonica is a collection of pedagogically-oriented open source software
that is broadly useful for image processing and image analysis applications. |
| levmar |
numlib |
Levmar is an implementation of Levenberg-Marquardt in C |
| lftp |
tools |
lftp is a sophisticated file transfer program supporting a number of network protocols. |
| lhapdf |
phys |
LHAPDF is a general purpose C++ interpolator, used for evaluating PDFs from discretised data files. |
| libassuan |
lib |
Libassuan is a small library implementing the so-called Assuan protocol. This protocol is used for IPC between most newer GnuPG components. |
| libevent |
lib |
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 |
lib |
Libfabric is a core component of OFI. It is the library that defines and exports
the user-space API of OFI, and is typically the only software that applications
deal with directly. It works in conjunction with provider libraries, which are
often integrated directly into libfabric.
|
| libgcrypt |
system |
Libgcrypt is a general purpose cryptographic library
originally based on code from GnuPG. It provides functions for all
cryptograhic building blocks: symmetric cipher algorithms (AES, Arcfour,
Blowfish, Camellia, CAST5, ChaCha20 DES, GOST28147, Salsa20, SEED,
Serpent, Twofish) and modes
(ECB,CFB,CBC,OFB,CTR,CCM,GCM,OCB,POLY1305,AESWRAP), hash algorithms
(MD2, MD4, MD5, GOST R 34.11, RIPE-MD160, SHA-1, SHA2-224, SHA2-256,
SHA2-384, SHA2-512, SHA3-224, SHA3-256, SHA3-384, SHA3-512, SHAKE-128,
SHAKE-256, TIGER-192, Whirlpool), MACs (HMAC for all hash algorithms,
CMAC for all cipher algorithms, GMAC-AES, GMAC-CAMELLIA, GMAC-TWOFISH,
GMAC-SERPENT, GMAC-SEED, Poly1305, Poly1305-AES, Poly1305-CAMELLIA,
Poly1305-TWOFISH, Poly1305-SERPENT, Poly1305-SEED), public key
algorithms (RSA, Elgamal, DSA, ECDSA, EdDSA, ECDH), large integer
functions, random numbers and a lot of supporting functions. |
| libgd |
lib |
GD is an open source code library for the dynamic creation of images by programmers. |
| libgeotiff |
lib |
Library for reading and writing coordinate system information from/to GeoTIFF files |
| libglade |
lib |
Libglade is a library for constructing user interfaces dynamically from XML descriptions. |
| libglu |
vis |
The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
| libgpg-error |
system |
Libgpg-error is a small library that defines common error values for all GnuPG components. |
| libgsf |
lib |
libgsf -- The G Structured File Library aims to provide an efficient extensible i/o abstraction for dealing with different structured file formats. |
| libgtextutils |
bio |
ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream |
| libharu |
lib |
libHaru is a free, cross platform, open source library for generating PDF files. |
| libibmad |
system |
libibmad is a convenience library to encode, decode, and dump IB MAD packets. It
is implemented on top of and in conjunction with libibumad (the umad kernel
interface library.) |
| libibumad |
system |
libibumad is the umad kernel interface library. |
| libint |
chem |
Libint - a library for the evaluation of molecular integrals of many-body operators over Gaussian functions |
| libksba |
lib |
Libksba is a library to make the tasks of working with X.509 certificates, CMS data and related objects more easy. |
| libmatheval |
lib |
GNU libmatheval is a library (callable from C and Fortran) to parse
and evaluate symbolic expressions input as text. |
| libpng |
lib |
libpng is the official PNG reference library |
| libreadline |
lib |
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.
|
| librmath |
lib |
The routines supporting the distribution and special functions in R and a few others are declared
in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications. |
| librsvg |
vis |
librsvg is a library to render SVG files using cairo. |
| libsndfile |
lib |
Libsndfile is a C library for reading and writing files containing sampled sound
(such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. |
| libspatialite |
lib |
SpatiaLite is an open source library intended to extend the SQLite core to support
fully fledged Spatial SQL capabilities. |
| libtool |
lib |
GNU libtool is a generic library support script. Libtool hides the complexity
of using shared libraries behind a consistent, portable interface.
|
| libxc |
chem |
Libxc is a library of exchange-correlation functionals for density-functional theory.
The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
| libxml2 |
lib |
Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable
outside of the Gnome platform). |
| libxsmm |
math |
LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications
targeting Intel Architecture (x86). |
| libyaml |
lib |
LibYAML is a YAML parser and emitter written in C. |
| lightgbm |
data |
LightGBM is a gradient boosting framework that uses tree based learning algorithms.
|
| llvm |
compiler |
The LLVM Core libraries provide a modern source- and target-independent
optimizer, along with code generation support for many popular CPUs
(as well as some less common ones!) These libraries are built around a well
specified code representation known as the LLVM intermediate representation
("LLVM IR"). The LLVM Core libraries are well documented, and it is
particularly easy to invent your own language (or port an existing compiler)
to use LLVM as an optimizer and code generator. |
| locuszoom |
bio |
LocusZoom Standalone is for the command line (standalone) version of LocusZoom, an application for creating regional plots from genome-wide association studies built in Python and R. |
| longranger |
bio |
Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. |
| macs2 |
bio |
With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing
(ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq
analysis method, we presented the Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding
sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS
improves the spatial resolution of binding sites through combining the information of both sequencing tag position and
orientation.
|
| maestro |
bio |
MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. MAESTRO combines several dozen tools and packages to create an integrative pipeline, which enables scRNA-seq and scATAC-seq analysis from raw sequencing data (fastq files) all the way through alignment, quality control, cell filtering, normalization, unsupervised clustering, differential expression and peak calling, celltype annotation and transcription regulation analysis.
|
| mafft |
bio |
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. |
| make |
%!s(<nil>) |
GNU version of make utility |
| manta |
bio |
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. |
| marge |
bio |
MARGE is a robust methodology that leverages a comprehensive library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse. |
| mathematica |
%!s(<nil>) |
|
| matlab |
%!s(<nil>) |
|
| maven |
devel |
Binary maven install, Apache Maven is a software project management and comprehension tool. Based on
the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a
central piece of information.
|
| mayavi |
vis |
A tool for easy and interactive visualization of data. |
| mcr |
math |
The MATLAB Runtime is a standalone set of shared libraries
that enables the execution of compiled MATLAB applications
or components on computers that do not have MATLAB installed. |
| meme |
%!s(<nil>) |
The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or
GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using
MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate
motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment
using SpaMo or CentriMo. |
| meson |
tools |
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. |
| metamorpheus |
bio |
MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. This program combines features of Morpheus and G-PTM-D in a single tool.
|
| metis |
math |
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 |
tools |
Micromamba is a small, pure-C++ executable with enough functionalities to bootstrap fully functional conda-environments. |
| mirdeep2 |
bio |
miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...). |
| moist |
tools |
moist is a Python database adaptor for MySQL, MariaDB, and (eventually) Drizzle. It is a continuation of the development fork of MySQLdb, i.e. pre-2.0. |
| mongosh |
tools |
The MongoDB Shell, mongosh, is a fully functional JavaScript and Node.js 14.x REPL environment for interacting with MongoDB deployments. You can use the MongoDB Shell to test queries and operations directly with your database. |
| mothur |
bio |
Mothur is a single piece of open-source, expandable software
to fill the bioinformatics needs of the microbial ecology community. |
| motif |
vis |
Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building
applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems.
It was the standard toolkit for the Common Desktop Environment and thus for Unix. |
| mpfr |
math |
The MPFR library is a C library for multiple-precision
floating-point computations with correct rounding. |
| mrtrix3 |
bio |
MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. It is designed with consistency, performance, and stability in mind, and is freely available under an open-source license. It is developed and maintained by a team of experts in the field, fostering an active community of users from diverse backgrounds. |
| mrtrix3tissue |
bio |
MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software. |
| multiqc |
bio |
MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. |
| mumax3 |
tools |
GPU accelerated micromagnetic simulator. |
| mummer |
bio |
MUMmer is a system for rapidly aligning entire genomes,
whether in complete or draft form. AMOS makes use of it. |
| muscle |
bio |
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. MUSCLE can align hundreds of sequences in seconds. Most users
learn everything they need to know about MUSCLE in a few minutes—only a handful of
command-line options are needed to perform common alignment tasks. |
| mutect |
bio |
MuTect is a method developed at the Broad Institute for the reliable
and accurate identification of somatic point mutations in next generation sequencing
data of cancer genomes. |
| mutsigcv |
bio |
MutSig stands for "Mutation Significance". MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes. |
| mysqlclient |
lib |
Python interface to MySQL |
| namd |
chem |
NAMD is a parallel molecular dynamics code designed for high-performance simulation of
large biomolecular systems. |
| nanopolish |
bio |
Software package for signal-level analysis of Oxford Nanopore sequencing data. |
| nasm |
lang |
NASM: General-purpose x86 assembler |
| ncbi-vdb |
bio |
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
using data in the INSDC Sequence Read Archives. |
| nccl |
%!s(<nil>) |
The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective
communication primitives that are performance optimized for NVIDIA GPUs. |
| ncdu |
tools |
Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a
remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular
desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like
environment with ncurses installed. |
| ncl |
data |
NCL is an interpreted language designed specifically for scientific data analysis and visualization. |
| ncurses |
devel |
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 |
vis |
Ncview is a visual browser for netCDF format files.
Typically you would use ncview to get a quick and easy, push-button
look at your netCDF files. You can view simple movies of the data,
view along various dimensions, take a look at the actual data values,
change color maps, invert the data, etc. |
| netcdf |
data |
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 module bundles the C++ and Fortran libaries. |
| netcdf-c |
data |
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. |
| netcdf-cxx |
data |
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. |
| netcdf-fortran |
data |
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. |
| netlogo |
math |
NetLogo is a multi-agent programmable modeling environment. It
is used by tens of thousands of students, teachers and researchers worldwide.
It also powers HubNet participatory simulations. It is authored by Uri Wilensky
and developed at the CCL. |
| netperf |
base |
None |
| neuron |
bio |
Empirically-based simulations of neurons and networks of neurons. |
| nextflow |
tools |
Nextflow is a reactive workflow framework and a programming DSL
that eases writing computational pipelines with complex data |
| ngs |
bio |
NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from
Next Generation Sequencing. |
| ngsf |
bio |
ngsF is a program to estimate per-individual inbreeding coefficients under a probabilistic framework that takes the uncertainty of genotype's assignation into account. It avoids calling genotypes by using genotype likelihoods or posterior probabilities. |
| nibabies |
bio |
NiBabies is an open-source software pipeline designed to process anatomical and functional magnetic resonance imaging data. A member of the NeuroImaging PREProcessing toolS (NiPreps) family, NiBabies is designed and optimized for human infants between 0-2 years old. |
| ninja |
tools |
Ninja is a small build system with a focus on speed. |
| nodejs |
lang |
Node.js is a platform built on Chrome's JavaScript runtime
for easily building fast, scalable network applications. Node.js uses an
event-driven, non-blocking I/O model that makes it lightweight and efficient,
perfect for data-intensive real-time applications that run across distributed devices. |
| npth |
lib |
nPth is a library to provide the GNU Pth API and thus a non-preemptive threads implementation. |
| nseg |
bio |
Nseg is used to identify low complexity sequencesi. |
| ntl |
math |
NTL is a high-performance, portable C++ library providing data structures and algorithms
for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the
integers and over finite fields. |
| numactl |
tools |
The numactl program allows you to run your application program on specific
cpu's and memory nodes. It does this by supplying a NUMA memory policy to
the operating system before running your program. The libnuma library provides
convenient ways for you to add NUMA memory policies into your own program.
|
| nvhpc |
%!s(<nil>) |
C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) |
| nvompic |
%!s(<nil>) |
NVHPC Compiler including OpenMPI for MPI support. |
| ocaml |
compiler |
OCaml is an industrial-strength programming language supporting functional, imperative and object-oriented styles |
| ocp-models |
chem |
ocp-models is the modeling codebase for the Open Catalyst Project. It provides implementations of state-of-the-art ML algorithms for catalysis that take arbitrary chemical structures as input to predict energy / forces / positions
|
| openbabel |
chem |
Open Babel is a chemical toolbox designed to speak the many
languages of chemical data. It's an open, collaborative project allowing anyone
to search, convert, analyze, or store data from molecular modeling, chemistry,
solid-state materials, biochemistry, or related areas. |
| openblas |
%!s(<nil>) |
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
| openbugs |
math |
OpenBUGS is a software application for the Bayesian analysis of complex statistical models using Markov chain Monte Carlo (MCMC) methods. |
| openfoam |
cae |
OpenFOAM is a free, open source CFD software package.
OpenFOAM has an extensive range of features to solve anything from complex fluid flows
involving chemical reactions, turbulence and heat transfer,
to solid dynamics and electromagnetics. |
| openjpeg |
lib |
OpenJPEG is an open-source JPEG 2000 codec written in C. |
| openmm |
chem |
OpenMM is a toolkit for molecular simulation using high performance GPU code.
|
| openmpi |
%!s(<nil>) |
The Open MPI Project is an open source MPI-3 implementation. |
| openms |
bio |
OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. |
| openslide |
bio |
OpenSlide is a C library that provides a simple interface to read whole-slide images. |
| openslide-python |
vis |
Python bindings for the OpenSlide libary |
| openspeedshop |
tool |
|
| openssl |
%!s(<nil>) |
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured,
and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1)
protocols as well as a full-strength general purpose cryptography library. |
| optix |
vis |
OptiX is NVIDIA SDK for easy ray tracing performance.
It provides a simple framework for accessing the GPU’s massive ray tracing
power using state-of-the-art GPU algorithms. |
| orca |
chem |
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry
with specific emphasis on spectroscopic properties of open-shell molecules.
It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single-
and multireference correlated ab initio methods.
It can also treat environmental and relativistic effects. |
| p3dfft |
numlib |
P3DFFT is a library for large-scale computer simulations on parallel platforms. |
| p4vasp |
chem |
Variation graphs provide a succinct encoding of the sequences of many genomes. |
| p7zip |
tools |
p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix.
7-Zip is a file archiver with highest compression ratio. |
| paintor |
bio |
PAINTOR is a statistical fine-mapping method that integrates functional genomic data with association strength from potentially multiple populations (or traits) to prioritize variants for follow-up analysis. |
| pandoc |
tools |
If you need to convert files from one markup format into another, pandoc is your swiss-army knife |
| parallel |
tools |
parallel: Build and execute shell commands in parallel |
| paraview |
vis |
ParaView is a scientific parallel visualizer. |
| parmetis |
numlib |
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. ParMETIS extends the
functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and
large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way
graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. |
| pasapipeline |
lib |
PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments. |
| patric |
bio |
PATRIC is an integration of different types of data and software tools that support research on bacterial pathogens. |
| pbwt |
bio |
The pbwt package provides a core implementation and development environment for PBWT (Positional Burrows-Wheeler Transform) methods for storing and computing on genome variation data sets. |
| pcmsolver |
chem |
An API for the Polarizable Continuum Model. |
| pcre |
devel |
The PCRE library is a set of functions that implement regular expression pattern matching using
the same syntax and semantics as Perl 5. |
| pcre2 |
devel |
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax
and semantics as Perl 5.
|
| peakseq |
bio |
PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq
experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from
a control experiment and outputs a file with peak regions ranked with increasing Q-values. |
| peer |
bio |
PEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. |
| perf |
tools |
Performance analysis tools for Linux |
| perl |
lang |
Larry Wall's Practical Extraction and Report Language |
| petsc |
numlib |
PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
scalable (parallel) solution of scientific applications modeled by partial differential equations. |
| pgi |
compiler |
C, C++ and Fortran compilers from The Portland Group - PGI |
| phonopy |
chem |
Phonopy is an open source package of phonon calculations based on the supercell approach.
Phono3py calculates phonon-phonon interaction and related properties using the supercell approach.
|
| picard |
bio |
A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| pigz |
tools |
pigz, which stands for parallel implementation of gzip, is a fully
functional replacement for gzip that exploits multiple processors and multiple
cores to the hilt when compressing data. pigz was written by Mark Adler, and
uses the zlib and pthread libraries.
|
| pipenv |
tools |
Pipenv is a tool that aims to bring the best of all packaging worlds (bundler, composer, npm, cargo, yarn, etc.) to the Python world. |
| platform-mpi |
mpi |
Platform MPI is an MPI-2 implementation from IBM. |
| plink |
bio |
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
| plumed |
chem |
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. Free energy calculations can be
performed as a function of many order parameters with a particular focus on biological problems, using
state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
|
| pmix |
%!s(<nil>) |
Process Management for Exascale Environments
PMI Exascale (PMIx) represents an attempt to
provide an extended version of the PMI standard specifically designed
to support clusters up to and including exascale sizes. The overall
objective of the project is not to branch the existing pseudo-standard
definitions - in fact, PMIx fully supports both of the existing PMI-1
and PMI-2 APIs - but rather to (a) augment and extend those APIs to
eliminate some current restrictions that impact scalability, and (b)
provide a reference implementation of the PMI-server that demonstrates
the desired level of scalability.
|
| pnetcdf |
data |
Parallel netCDF: A Parallel I/O Library for NetCDF File Access |
| pompi |
toolchain |
Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI. |
| poppler |
vis |
Poppler is a PDF rendering library based on the xpdf-3.0 code
base. |
| postgresql |
data |
PostgreSQL is a powerful, open source object-relational
database system. It is fully ACID compliant, has full support for foreign
keys, joins, views, triggers, and stored procedures (in multiple languages).
It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN,
CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of
binary large objects, including pictures, sounds, or video. It has native
programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC,
among others, and exceptional documentation. |
| pov-ray |
vis |
The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program
which generates images from a text-based scene description, and is available for a variety
of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning
three-dimensional graphics. The source code is available for those wanting to do their own ports. |
| proj |
%!s(<nil>) |
Program proj is a standard Unix filter function which converts
geographic longitude and latitude coordinates into cartesian coordinates |
| prokka |
bio |
Prokka is a software tool for the rapid annotation of prokaryotic genomes. |
| proteowiz |
bio |
ProteoWizard provides a set of open-source, cross-platform software libraries and tools (e.g. msconvert, Skyline, IDPicker, SeeMS) that facilitate proteomics data analysis. The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. |
| protobuf |
devel |
Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data. |
| psipred |
bio |
The PSIPRED Workbench provides a range of protein structure prediction methods. |
| pslib |
tools |
pslib is a C-library to create PostScript files on the fly. It offers many drawing primitives, inclusion of png and eps images and a very sophisticated text rendering including hyphenation, kerning and ligatures. |
| psmc |
bio |
PSMC infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. |
| pybind11 |
lib |
pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
mainly to create Python bindings of existing C++ code. |
| pycairo |
vis |
Python bindings for the cairo library |
| pygobject |
vis |
Python Bindings for GLib/GObject/GIO/GTK+ |
| pygtk |
vis |
PyGTK lets you to easily create programs with a graphical user interface
using the Python programming language. |
| pyopengl |
vis |
PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. |
| python |
lang |
Intel Distribution for Python. Powered by Anaconda.
Accelerating Python* performance on modern architectures from Intel.
|
| pytorch |
data |
PyTorch is a deep learning framework that puts Python first. It provides Tensors and Dynamic neural networks in Python with strong GPU acceleration.
|
| pyyaml |
lib |
PyYAML is a YAML parser and emitter for the Python programming language. |
| qiime |
bio |
QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. |
| qiime2 |
bio |
QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
|
| qt5 |
devel |
Qt is a comprehensive cross-platform C++ application framework. |
| qt5webkit |
%!s(<nil>) |
Qt Port of WebKit. WebKit is an open source web browser engine. |
| qtltools |
bio |
QTLtools is a tool set for molecular QTL discovery and analysis.
It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs)
in few easy-to-perform steps. |
| qualimap |
bio |
Qualimap 2 is a platform-independent application written in Java and R that provides both
a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of
alignment sequencing data and its derivatives like feature counts. |
| quantumespresso |
chem |
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. |
| qwt |
lib |
The Qwt library contains GUI Components and utility classes which are primarily useful for programs
with a technical background. |
| rapidsai |
data |
The RAPIDS suite of open source software libraries and APIs gives you the ability to execute end-to-end data science and analytics pipelines entirely on GPUs. Licensed under Apache 2.0, RAPIDS is incubated by NVIDIA based on extensive hardware and data science science experience. RAPIDS utilizes NVIDIA CUDA primitives for low-level compute optimization, and exposes GPU parallelism and high-bandwidth memory speed through user-friendly Python interfaces.
|
| rasqual |
bio |
RASQUAL (Robust Allele Specific QUAntification and quality controL) maps QTLs for sequenced based cellular traits by combining population and allele-specific signals. |
| raxml |
bio |
RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. |
| rclone |
tools |
Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers. |
| rdp-classifier |
bio |
The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic
assignments from domain to genus, with confidence estimates for each assignment. |
| readosm |
lib |
ReadOSM is an open source library to extract valid data from within an Open Street Map input file. |
| redis-cli |
tools |
Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker.
|
| reframe |
devel |
ReFrame is a framework for writing regression tests for HPC systems. |
| relion |
bio |
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). |
| remora |
tools |
REsource MOnitoring for Remote Applications |
| repast_hpc |
lang |
Repast for High Performance Computing (Repast HPC) is a next generation agent-based modeling system intended for large-scale distributed computing platforms. |
| rip-md |
bio |
RIP-MD allows to apply Residue Interaction Networks (RINs) to the analysis of molecular dynamics simulations of protein. |
| rmats-turbo |
bio |
rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). The major difference between rMATS turbo and rMATS is speed and space usage. rMATS turbo is 100 times faster and the output file is 1000 times smaller than rMATS. These advantages make analysis and storage of a large scale dataset easy and convenient.
|
| rosetta |
bio |
The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.
It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme
design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. |
| rsem |
bio |
RNA-Seq by Expectation-Maximization |
| rstudio |
lang |
RStudio is a set of integrated tools designed to help you be more productive with R. |
| ruby |
lang |
Ruby is a dynamic, open source programming language with
a focus on simplicity and productivity. It has an elegant syntax that is
natural to read and easy to write. |
| rust |
lang |
Rust is a systems programming language that runs blazingly fast, prevents segfaults,
and guarantees thread safety. |
| sagemath |
data |
SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. |
| saint |
%!s(<nil>) |
Significance Analysis of INTeractome (SAINT) consists of a series of software tools for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments. |
| saintexpress |
%!s(<nil>) |
Significance Analysis of INTeractome (SAINT) consists of a series of software tools for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments. |
| salmon |
bio |
Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimates from RNA-seq data. |
| sambamba |
bio |
Sambamba is a tool for processing BAM files. |
| samtools |
bio |
SAM Tools provide various utilities for manipulating alignments in the SAM format,
including sorting, merging, indexing and generating alignments in a per-position format. |
| sas |
math |
Statistical analysis package |
| sbt |
lang |
A build tool for Scala. |
| scalapack |
%!s(<nil>) |
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
redesigned for distributed memory MIMD parallel computers. |
| scons |
devel |
SCons is a software construction tool. |
| scotch |
math |
Software package and libraries for sequential and parallel graph partitioning,
static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. |
| sdl2 |
lib |
SDL: Simple DirectMedia Layer, a cross-platform multimedia library |
| seacr |
bio |
SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes (i.e. regions with no read coverage). |
| seqoutbias |
%!s(<nil>) |
Molecular biology enzymes have nucleic acid preferences for their substrates; the preference of an
enzyme is typically dictated by the sequence at or near the active site of the enzyme. This bias may result
in spurious read count patterns when used to interpret high-resolution molecular genomics data. The
seqOutBias program aims to correct this issue by scaling the aligned read counts by the ratio of genome-wide
observed read counts to the expected sequence based counts for each k-mer.
|
| sga |
bio |
SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.
|
| sgp |
data |
Gossip-based distributed optimization algorithms implemented in PyTorch
|
| shapeit |
bio |
SHAPEIT is a fast and accurate method for estimation of
haplotypes (aka phasing) from genotype or sequencing data. |
| shapeit4 |
bio |
SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. The version 4 is a refactored and improved version of the SHAPEIT algorithm. |
| shapelib |
lib |
The Shapefile C Library provides the ability to write simple C programs for reading, writing and updating (to a limited extent) ESRI Shapefiles, and the associated attribute file (.dbf). |
| shengbte |
chem |
ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. |
| sibil-env |
vis |
This module sets up the environment for the SIBIL application. |
| sicerpy |
bio |
SICER.py is a Python wrapper for the SICER peak caller software. |
| siesta |
%!s(<nil>) |
SIESTA is both a method and its computer program implementation, to perform efficient electronic
structure calculations and ab initio molecular dynamics simulations of molecules and solids. |
| silo |
data |
Silo is a library for reading and writing a wide variety of scientific data to binary, disk files |
| singularity |
containersystem |
Singularity enables users to have full control of their environment. Singularity containers can be used to package entire scientific workflows, software and libraries, and even data. |
| skopeo |
tools |
skopeo is a command line utility that performs various operations on container images and image repositories.
|
| slatec |
numlib |
Fortran 77 numerical library. |
| slepc |
numlib |
SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution
of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for
either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a
partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. |
| slicer |
tools |
3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. |
| slim |
bio |
SLiM is an evolutionary simulation package that provides facilities for very easily and quickly constructing genetically explicit individual-based evolutionary models. |
| smrtlink |
bio |
PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule,
Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI
or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through
the extensive set of APIs provided |
| snakemake |
tools |
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. |
| snap |
bio |
SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. |
| snap-stanford |
vis |
Snap.py is a Python interface for SNAP. SNAP is a general purpose, high performance system for analysis and manipulation of large networks. SNAP is written in C++ and optimized for maximum performance and compact graph representation. It easily scales to massive networks with hundreds of millions of nodes, and billions of edges. |
| sortmerna |
bio |
SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. |
| spaceranger |
%!s(<nil>) |
A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting. |
| spack |
devel |
Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific
software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers,
and all of these builds can coexist on the same machine. |
| spades |
bio |
SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. |
| sparc |
%!s(<nil>) |
Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads |
| spark |
devel |
Spark is Hadoop MapReduce done in memory |
| sparseassembler |
bio |
A sparse graph approach to de novo genome assembly |
| sparsehash |
lib |
An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. |
| spglib |
lib |
Spglib is a library for finding and handling crystal symmetries written in C. |
| sprng |
lib |
Scalable Parallel Pseudo Random Number Generators Library |
| sqlite |
devel |
SQLite: SQL Database Engine in a C Library |
| sratoolkit |
bio |
The SRA Toolkit, and the source-code SRA System Development
Kit (SDK), will allow you to programmatically access data housed within SRA
and convert it from the SRA format |
| stacks |
bio |
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
|
| star |
bio |
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. |
| stata |
math |
Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. |
| stringtie |
bio |
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. |
| subversion |
tools |
Subversion is an open source version control system.
|
| suitesparse |
numlib |
SuiteSparse is a collection of libraries manipulate sparse matrices. |
| sundials |
math |
SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers |
| superlu |
numlib |
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations. |
| superlu_mt |
numlib |
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations. |
| swig |
devel |
SWIG is a software development tool that connects programs written in C and C++ with
a variety of high-level programming languages. |
| szip |
%!s(<nil>) |
Szip compression software, providing lossless compression of scientific data |
| tabix |
bio |
Generic indexer for TAB-delimited genome position files |
| taggraph |
bio |
TagGraph is a computational tool that provides an unrestricted string-based search method that is as much as 350-fold faster than existing approaches, and a probabilistic validation model that was optimized for post-translational modification assignments. |
| tbb |
lib |
Intel(R) Threading Building Blocks (Intel(R) TBB) makes parallel performance and scalability accessible to software developers who are writing loop- and task-based applications. Build robust applications that abstract platform details and threading mechanisms while achieving performance that scales with increasing core count. |
| tensorflow |
data |
TensorFlow is an open-source software library for Machine Intelligence.
|
| tesseract |
vis |
Tesseract is an optical character recognition engine |
| texinfo |
devel |
Texinfo is the official documentation format of the GNU project. |
| texlive |
tools |
TeX Live is intended to be a straightforward 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.
|
| thermorawfileparser |
bio |
Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono (works on Windows too). |
| thirdorder |
chem |
Python package for creating input for ShengBTE. |
| tmux |
tools |
tmux is a terminal multiplexer. It lets you switch easily
between several programs in one terminal, detach them (they keep
running in the background) and reattach them to a different terminal. |
| tophat |
bio |
TopHat is a fast splice junction mapper for RNA-Seq reads. |
| torus |
bio |
TORUS - QTL Discovery utilizing Genomic Annotations is a free software package that implements a computational procedure for discovering molecular QTLs incorporating genomic annotations. |
| totalview |
debugger |
TotalView is a GUI-based source code defect analysis tool that gives you unprecedented
control over processes and thread execution and visibility into program state and variables. It allows
you to debug one or many processes and/or threads in a single window with complete control over program
execution. This allows you to set breakpoints, stepping line by line through the code on a single thread,
or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads.
You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take
advantage of threads, OpenMP, MPI, GPUs or coprocessors. |
| tree |
tools |
Tree is a recursive directory listing command that produces a depth indented listing of files, which is colorized ala dircolors if the LS_COLORS environment variable is set and output is to tty. |
| trimgalore |
bio |
Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. |
| trimmomatic |
bio |
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. |
| trinity |
%!s(<nil>) |
Trinity 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. |
| ucc |
%!s(<nil>) |
UCC (Unified Collective Communication) is a collective
communication operations API and library that is flexible, complete, and
feature-rich for current and emerging programming models and runtimes.
|
| ucsc-tools |
bio |
A set of genome utilities developed at the University of California Santa Cruz. |
| ucx |
%!s(<nil>) |
Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications
|
| ucx-cuda |
%!s(<nil>) |
Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications
This module adds the UCX CUDA support.
|
| udunits |
tools |
UDUNITS supports conversion of unit specifications between formatted and binary forms,
arithmetic manipulation of units, and conversion of values between compatible scales of measurement. |
| unrar |
tools |
RAR is a powerful archive manager. |
| util-linux |
tools |
Set of Linux utilities |
| vapor |
vis |
VAPOR is the Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers. VAPOR provides an interactive 3D visualization environment that can also produce animations and still frame images |
| varscan |
bio |
VarScan - Variant calling and somatic mutation/CNV detection for next-generation sequencing data |
| vasp |
chem |
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling. |
| vcell |
bio |
VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application. |
| vcftools |
bio |
The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. |
| velvet |
bio |
Sequence assembler for very short reads |
| vg |
bio |
Variation graphs provide a succinct encoding of the sequences of many genomes. |
| viennarna |
bio |
The Vienna RNA Package consists of a C code library and several
stand-alone programs for the prediction and comparison of RNA secondary structures. |
| vigra |
vis |
VIGRA stands for "Vision with Generic Algorithms". It's an image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images, because many algorithms (e.g. filters, feature computation, superpixels) are implemented for arbitrary high dimensions. |
| visit |
vis |
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. |
| vmd |
chem |
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. |
| voro++ |
math |
Voro++ is a software library for carrying out three-dimensional computations of the Voronoi
tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations,
computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that
rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used
to analyze a system of particles. |
| vsearch |
bio |
VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. |
| vtk |
vis |
The Visualization Toolkit (VTK) is an open-source, freely available software system for
3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several
interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization
algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques
such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. |
| wannier90 |
chem |
Wannier90 is a package to calculate maximally-localised Wannier functions. |
| wasp |
bio |
WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs. |
| wdltool |
tools |
A Java command-line tool co-developed with WDL that performs utility functions, including syntax validation and generation of input JSON templates. |
| wigtobigwig |
bio |
The bigWig format is useful for dense, continuous data that will be displayed in the Genome Browser as a graph.
BigWig files are created from wiggle (wig) type files using the program wigToBigWig.
|
| wxpython |
vis |
wxPython is a GUI toolkit for the Python programming language.
It allows Python programmers to create programs with a robust,
highly functional graphical user interface, simply and easily.
It is implemented as a Python extension module (native code)
that wraps the popular wxWidgets cross platform GUI library,
which is written in C++. |
| wxwidgets |
vis |
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 platform's native API rather than emulating the GUI. |
| x264 |
vis |
x264 is a free software library and application for encoding video streams
into the H.264/MPEG-4 AVC compression format, and is released under the
terms of the GNU GPL.
|
| x265 |
vis |
x265 is a free software library and application for encoding video streams
into the H.265 AVC compression format, and is released under the terms of
the GNU GPL.
|
| xcrysden |
vis |
XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. |
| xerces |
tools |
Xerces-C++ is a validating XML parser written in a portable subset of C++. |
| xxdiff |
tools |
xxdiff is a graphical file and directories comparator and merge tool. |
| xz |
tools |
xz: XZ utilities |
| yaff |
chem |
Yaff stands for 'Yet another force field'. It is a pythonic force-field code. |
| yambo |
phys |
YAMBO implements Many-Body Perturbation Theory (MBPT) methods (such as GW and BSE) and Time-Dependent Density Functional Theory (TDDFT), which allows for accurate prediction of fundamental properties as band gaps of semiconductors, band alignments, defect quasi-particle energies, optics and out-of-equilibrium properties of materials. |
| yasm |
lang |
Yasm: Complete rewrite of the NASM assembler with BSD license |
| z3 |
%!s(<nil>) |
Z3 is a theorem prover from Microsoft Research.
|
| zlib |
lib |
zlib is designed to be a free, general-purpose, legally unencumbered -- that is,
not covered by any patents -- lossless data-compression library for use on virtually any
computer hardware and operating system. |
| zstd |
lib |
Zstandard is a real-time compression algorithm, providing high compression ratios.
It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder.
It also offers a special mode for small data, called dictionary compression, and can create dictionaries
from any sample set. |
