| 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.
|
| abseil |
lib |
Abseil is an open-source collection of C++ library code designed to augment the
C++ standard library. The Abseil library code is collected from Google's own
C++ code base, has been extensively tested and used in production, and is the
same code we depend on in our daily coding lives. |
| 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 - an approximate GREP. |
| 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
|
| alphapulldown |
bio |
AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer |
| amber |
chem |
Amber (originally Assisted Model Building with Energy Refinement) is software for performing
molecular dynamics and structure prediction. |
| amptorch |
chem |
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 |
This module points to Miniforge.
- The conda/mamba executables are included.
- The default channel is conda-forge.
For details see https://www.rc.virginia.edu/2024/10/transition-from-anaconda-to-miniforge-october-15-2024/
|
| 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 |
bio |
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.
|
| aocc |
compiler |
AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM |
| aompi |
toolchain |
AMD Optimizing C/C++ and Fortran Compilers (AOCC)
including OpenMPI for MPI support. |
| apptainer |
tools |
Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal
of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should
be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux
version differences between the source and target systems. |
| archspec |
tools |
A library for detecting, labeling, and reasoning about microarchitectures |
| aria2 |
tools |
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. |
| at-spi2-atk |
vis |
AT-SPI 2 toolkit bridge |
| at-spi2-core |
vis |
Assistive Technology Service Provider Interface.
|
| 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.
|
| attrdict3 |
lib |
AttrDict is a Python library that provides mapping objects that allow their elements
to be accessed both as keys and as attributes. |
| augustus |
bio |
AUGUSTUS is a program to find genes and their structures in one or more genomes. |
| autoconf |
devel |
Autoconf is an extensible package of M4 macros that produce shell scripts
to automatically configure software source code packages. These scripts can
adapt the packages to many kinds of UNIX-like systems without manual user
intervention. Autoconf creates a configuration script for a package from a
template file that lists the operating system features that the package can
use, in the form of M4 macro calls.
|
| awscli |
tools |
This package provides a unified command line interface to Amazon Web Services.
|
| axel |
tools |
Lightweight CLI download accelerator |
| 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 |
devel |
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 enables the development of custom data management
solutions, without the overhead traditionally associated with such custom
projects. |
| 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. |
| binutils |
tools |
binutils: GNU binary utilities |
| 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 |
bio |
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 |
devel |
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. |
| bracken |
bio |
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. |
| 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. |
| 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.
|
| cellpose |
bio |
a generalist algorithm for cellular segmentation |
| 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 |
bio |
A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting. |
| cellranger-arc |
bio |
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. |
| cereal |
lib |
cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly
turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be
fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or
used standalone. |
| 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. |
| cfitsio |
lib |
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in
FITS (Flexible Image Transport System) data format. |
| 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. |
| ciftilib |
lib |
C++ Library for reading and writing CIFTI-2 and CIFTI-1 files |
| 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 |
compiler |
C, C++, Objective-C compiler, based on LLVM. Does not
include C++ standard library -- use libstdc++ from GCC. |
| 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. |
| cloudcompare |
geo |
3D point cloud and mesh processing software |
| 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. |
| 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. |
| cryosparc |
data |
CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.
|
| 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. |
| 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 |
bio |
Cytoscape is an open source software platform for visualizing
complex networks and integrating these with any type of attribute data.
A lot of Apps are available for various kinds of problem domains,
including bioinformatics, social network analysis, and semantic web. |
| danpos |
bio |
A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2. |
| datamash |
data |
GNU datamash performs basic numeric, textual and statistical operations on input data files |
| db_file |
data |
Perl5 access to Berkeley DB version 1.x. |
| dbg2olc |
bio |
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. |
| dbus |
devel |
D-Bus is a message bus system, a simple way for applications to talk
to one another. In addition to interprocess communication, D-Bus helps
coordinate process lifecycle; it makes it simple and reliable to code
a "single instance" application or daemon, and to launch applications
and daemons on demand when their services are needed.
|
| 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 |
bio |
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 |
bio |
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. |
| dotnet-sdk |
lang |
.NET is a free, cross-platform, open source developer platform for building many different types
of applications. |
| double-conversion |
lib |
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. |
| 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). |
| 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. |
| elfutils |
lib |
The elfutils project provides libraries and tools for ELF files
and DWARF data.
|
| elpa |
math |
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. |
| 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 a suite of software tools for developing
high-performance, multi-component Earth science modeling applications. |
| 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. |
| expat |
tools |
Expat is an XML parser library written in C. It is a stream-oriented parser
in which an application registers handlers for things the parser might find
in the XML document (like start tags). |
| 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. |
| fastx-toolkit |
bio |
The FASTX-Toolkit is a collection of command line tools for
Short-Reads FASTA/FASTQ files preprocessing. |
| ffmpeg |
vis |
A complete, cross-platform solution to record, convert and stream audio and video. |
| fftw |
numlib |
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. |
| fgwas |
lib |
fgwas is a command line tool for integrating functional genomic information into a genome-wide association study (GWAS). |
| fiji |
vis |
Fiji is an image processing package—a 'batteries-included' distribution of
ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
This release is based on ImageJ-2.1.0 and Fiji-2.1.1 |
| 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). |
| fontconfig |
vis |
Fontconfig is a library designed to provide system-wide font configuration,
customization and application access.
|
| 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. |
| freetype |
vis |
FreeType 2 is a software font engine that is designed to be small, efficient,
highly customizable, and portable while capable of producing high-quality
output (glyph images). It can be used in graphics libraries, display servers,
font conversion tools, text image generation tools, and many other products
as well.
|
| 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. |
| g2clib |
data |
Library contains GRIB2 encoder/decoder ('C' version). |
| g2lib |
data |
Library contains GRIB2 encoder/decoder and search/indexing routines. |
| 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,...). |
| 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. |
| 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. |
| gdk-pixbuf |
vis |
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation.
It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it
was distributed as part of GTK+ 2 but it was split off into a separate package
in preparation for the change to GTK+ 3.
|
| gdrcopy |
lib |
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) |
| gettext |
tools |
GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may
build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools
and documentation |
| 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). |
| ghc |
compiler |
The Glorious/Glasgow Haskell Compiler |
| 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. |
| giflib |
lib |
giflib is a library for reading and writing gif images.
It is API and ABI compatible with libungif which was in wide use while
the LZW compression algorithm was patented. |
| git-annex |
tools |
git-annex allows managing large files with git, without storing the file contents in git. It can sync,
backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the
power and distributed nature of git to bear on your large files with git-annex. |
| 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 |
| gl2ps |
vis |
GL2PS: an OpenGL to PostScript printing library |
| 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. |
| glpk |
tools |
The GLPK (GNU Linear Programming Kit) package is intended for
solving large-scale linear programming (LP),
mixed integer programming (MIP), and other related problems.
It is a set of routines written in ANSI C
and organized in the form of a callable library. |
| 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. |
| gmvapich2 |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain,
including MVAPICH2 for MPI support. |
| 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. |
| gocryptfs |
devel |
An encrypted overlay filesystem written in Go.
gocryptfs is built on top the excellent go-fuse FUSE library.
|
| gompi |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit,
including OpenMPI for MPI support. |
| 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. |
| gperf |
base |
None |
| 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 |
bio |
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. |
| grackle |
astro |
Grackle is a chemistry and radiative cooling library for astrophysical simulations and models. Grackle has interfaces for C, C++, Fortran, and Python codes |
| graphene |
lib |
Graphene is a thin layer of types for graphic libraries |
| 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 |
| 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. |
| gsea |
bio |
Gene Set Enrichment Analysis (GSEA) is a computational method that
determines whether an a priori defined set of genes shows statistically
significant, concordant differences between two biological states
(e.g. phenotypes). |
| 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. |
| gst-plugins-base |
vis |
GStreamer is a library for constructing graphs of media-handling
components. The applications it supports range from simple
Ogg/Vorbis playback, audio/video streaming to complex audio
(mixing) and video (non-linear editing) processing. |
| gstreamer |
vis |
GStreamer is a library for constructing graphs of media-handling
components. The applications it supports range from simple
Ogg/Vorbis playback, audio/video streaming to complex audio
(mixing) and video (non-linear editing) processing. |
| gtk3 |
vis |
GTK+ is the primary library used to construct user interfaces in GNOME. It
provides all the user interface controls, or widgets, used in a common
graphical application. Its object-oriented API allows you to construct
user interfaces without dealing with the low-level details of drawing and
device interaction.
|
| 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 |
| h5py |
data |
HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
amounts of data. |
| harfbuzz |
vis |
HarfBuzz is an OpenType text shaping engine. |
| hdf |
data |
HDF (also known as HDF4) is a library and multi-object file format for storing and managing data
between machines. |
| hdf5 |
data |
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. |
| 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 |
system |
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.
|
| 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. |
| 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 |
toolchain |
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 |
numlib |
Intel oneAPI Math Kernel Library |
| imkl-fftw |
numlib |
FFTW interfaces using Intel oneAPI Math Kernel Library |
| impi |
mpi |
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 |
| intel |
toolchain |
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. |
| 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 |
| itk |
data |
Insight Segmentation and Registration Toolkit (ITK) provides
an extensive suite of software tools for registering and segmenting
multidimensional imaging data. |
| 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. |
| jbigkit |
vis |
JBIG-KIT is a software implementation of the JBIG1 data
compression standard (ITU-T T.82), which was designed for bi-level image
data, such as scanned documents. |
| jcuda |
bio |
Java bindings for NVIDIA CUDA and related libraries. |
| jdftx |
phys |
JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. |
| jellyfish |
bio |
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. |
| jemalloc |
lib |
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and
scalable concurrency support. |
| jq |
tools |
jq is a lightweight and flexible command-line JSON processor. |
| json-c |
lib |
JSON-C implements a reference counting object model that allows you to easily construct JSON objects
in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON
objects. |
| 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. |
| juicebox |
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 |
| junit |
devel |
A programmer-oriented testing framework for Java. |
| jupyterlab |
tools |
JupyterLab is the latest web-based interactive development environment for notebooks, code, and data.
Its flexible interface allows users to configure and arrange workflows in data science, scientific
computing, computational journalism, and machine learning. A modular design invites extensions to
expand and enrich functionality.
|
| 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. |
| kent-tools |
bio |
A set of genome utilities developed at the University of California Santa Cruz. |
| 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. |
| 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 stands for Large-scale Atomic/Molecular Massively Parallel Simulator.
LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers.
|
| lammps_allegro |
chem |
Custom LAMMPS-Allegro module for Paolucci group |
| lammps_flare |
chem |
Custom LAMMPS-Flare module for Paolucci group |
| 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. |
| libaec |
lib |
Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers
(samples). The library achieves best results for low entropy data as often encountered in space imaging
instrument data or numerical model output from weather or climate simulations. While floating point representations
are not directly supported, they can also be efficiently coded by grouping exponents and mantissa. |
| libarchive |
tools |
Multi-format archive and compression library
|
| libdeflate |
system |
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. |
| libdrm |
lib |
Direct Rendering Manager runtime library. |
| libepoxy |
lib |
Epoxy is a library for handling OpenGL function pointer management for you |
| 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.
|
| libffi |
lib |
The libffi library provides a portable, high level programming interface to
various calling conventions. This allows a programmer to call any function
specified by a call interface description at run-time. |
| 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 |
| libglu |
vis |
The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
| libglvnd |
lib |
libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. |
| 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. |
| libiconv |
lib |
Libiconv converts from one character encoding to another through Unicode conversion |
| libint |
chem |
Libint - a library for the evaluation of molecular integrals of many-body operators over Gaussian functions |
| libjpeg-turbo |
lib |
libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to
accelerate baseline JPEG compression and decompression. libjpeg is a library
that implements JPEG image encoding, decoding and transcoding.
|
| libmatheval |
lib |
GNU libmatheval is a library (callable from C and Fortran) to parse
and evaluate symbolic expressions input as text. |
| libpciaccess |
system |
Generic PCI access library. |
| 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. |
| librttopo |
lib |
The RT Topology Library exposes an API to create and
manage standard (ISO 13249 aka SQL/MM) topologies using user-provided
data stores. |
| libspatialite |
lib |
SpatiaLite is an open source library intended to extend the SQLite core to support
fully fledged Spatial SQL capabilities. |
| libtiff |
lib |
tiff: Library and tools for reading and writing TIFF data files |
| libtirpc |
lib |
Libtirpc is a port of Suns Transport-Independent RPC library to Linux. |
| libtorch |
data |
A binary distribution of all headers, libraries and CMake configuration files required to depend on PyTorch. |
| libunwind |
lib |
The primary goal of libunwind is to define a portable and efficient C programming interface
(API) to determine the call-chain of a program. The API additionally provides the means to manipulate the
preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain
(non-local goto). The API supports both local (same-process) and remote (across-process) operation.
As such, the API is useful in a number of applications |
| 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. |
| libxml++ |
lib |
libxml++ is a C++ wrapper for the libxml XML parser library. |
| 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). |
| 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. |
| lpsolve |
math |
Mixed Integer Linear Programming (MILP) solver |
| 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 |
devel |
GNU version of make utility |
| mako |
devel |
A super-fast templating language that borrows the best ideas from the existing templating languages |
| 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.
|
| maxquant |
bio |
MaxQuant is a quantitative proteomics software package designed for analyzing large
mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling
techniques as well as label-free quantification are supported. |
| 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 |
bio |
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. |
| mesa |
vis |
Mesa is an open-source implementation of the OpenGL specification -
a system for rendering interactive 3D graphics. |
| 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. |
| miniforge |
lang |
Miniforge is a free minimal installer for conda and Mamba specific
to conda-forge. |
| minizip |
lib |
Mini zip and unzip based on zlib |
| mirdeep2 |
bio |
miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...). |
| mm-common |
devel |
The mm-common module provides the build infrastructure and
utilities shared among the GNOME C++ binding libraries. |
| 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.
|
| mpi4py |
lib |
MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for
the Python programming language, allowing any Python program to exploit multiple processors. |
| 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. |
| mvapich2 |
mpi |
The MVAPICH2 software, based on MPI 3.1 standard, delivers the best performance, scalability and fault tolerance for high-end computing systems and servers using InfiniBand, Omni-Path, Ethernet/iWARP, and RoCE networking technologies. |
| 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 |
lib |
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. |
| nlopt |
numlib |
NLopt is a free/open-source library for nonlinear optimization,
providing a common interface for a number of different free optimization routines
available online as well as original implementations of various other algorithms. |
| 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. |
| nseg |
bio |
Nseg is used to identify low complexity sequencesi. |
| nspr |
lib |
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level
and libc-like functions. |
| nss |
lib |
Network Security Services (NSS) is a set of libraries designed to support cross-platform development
of security-enabled client and server applications. |
| 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 |
compiler |
C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) |
| nvompi |
toolchain |
NVHPC Compiler including OpenMPI for MPI support. |
| nvshmem |
devel |
NVSHMEM is a parallel programming interface based on OpenSHMEM that provides
efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a
global address space for data that spans the memory of multiple GPUs and can be
accessed with fine-grained GPU-initiated operations, CPU-initiated operations,
and operations on CUDA streams.
|
| nvtop |
tools |
htop-like GPU usage monitor |
| 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 |
numlib |
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 |
mpi |
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. |
| opensim |
data |
OpenSim is software that lets users develop models of musculoskeletal structures and create dynamic simulations of movement |
| openslide |
vis |
OpenSlide is a C library that provides a simple interface to
read whole-slide images (also known as virtual slides). |
| openslide-python |
vis |
Python bindings for the OpenSlide libary |
| openspeedshop |
tool |
|
| 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. |
| pango |
vis |
Pango is a library for laying out and rendering of text, with an emphasis on internationalization.
Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the
context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. |
| 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. |
| pasapipeline |
bio |
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. |
| 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. |
| 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. |
| 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. |
| pixman |
vis |
Pixman is a low-level software library for pixel manipulation, providing
features such as image compositing and trapezoid rasterization. Important
users of pixman are the cairo graphics library and the X server.
|
| pkgconf |
devel |
pkgconf is a program which helps to configure compiler and linker flags for development libraries.
It is similar to pkg-config from freedesktop.org. |
| 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 |
lib |
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 |
| 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 |
lib |
Program proj is a standard Unix filter function which converts
geographic longitude and latitude coordinates into cartesian coordinates |
| 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. |
| protobuf-python |
devel |
Python Protocol Buffers runtime library. |
| prrte |
lib |
PRRTE is the PMIx Reference RunTime Environment |
| 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. |
| pymol |
vis |
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. |
| pyspark |
devel |
PySpark is the Python API for Apache Spark. It enables you to perform real-time, large-scale data processing in a distributed environment using Python. It also provides a PySpark shell for interactively analyzing your data. |
| 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.
|
| qgis |
geo |
A Free and Open Source Geographic Information System |
| qt5 |
devel |
Qt is a comprehensive cross-platform C++ application framework. |
| 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. |
| re2c |
tools |
re2c is a free and open-source lexer generator for C and C++. Its main goal is generating
fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using
traditional table-driven approach, re2c encodes the generated finite state automata directly in the form
of conditional jumps and comparisons. |
| 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. |
| regtools |
bio |
RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a
regulatory and splicing context. |
| 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). |
| 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.
|
| root |
data |
The ROOT system provides a set of OO frameworks with all the functionality
needed to handle and analyze large amounts of data in a very efficient way. |
| 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-server |
lang |
RStudio is an integrated development environment (IDE) for the R programming language. |
| 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 |
bio |
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 |
bio |
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 |
numlib |
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 |
bio |
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
|
| 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. |
| siesta |
chem |
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 |
| 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-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. |
| snappy |
lib |
Snappy is a compression/decompression library. It does not aim
for maximum compression, or compatibility with any other compression library;
instead, it aims for very high speeds and reasonable compression. |
| soci |
lang |
SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the
regular C++ code, staying entirely within the Standard C++. |
| sortmerna |
bio |
SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. |
| spaceranger |
bio |
A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting. |
| spades |
bio |
SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. |
| sparc |
bio |
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 |
| stack |
devel |
Stack is a cross-platform program for developing Haskell projects.
It is intended for Haskellers both new and experienced. |
| 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 |
tools |
Szip compression software, providing lossless compression of scientific data |
| tbb |
lib |
Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that
take full advantage of multicore performance, that are portable, composable and have future-proof scalability. |
| tensorflow |
data |
TensorFlow is an open-source software library for Machine Intelligence.
|
| tensorrt |
lib |
NVIDIA TensorRT is a platform for high-performance deep learning inference |
| 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 |
A Python script to help create input files for computing anhamonic
interatomic force constants, harnessing the symmetries of the system to minimize the
number of required DFT calculations. A second mode of operation allows the user to
build the third-order IFC matrix from the results of those runs. |
| 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. |
| togl |
vis |
Togl is a Tk widget for OpenGL rendering |
| 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. |
| trf |
bio |
Tandem Repeats Finder: a program to analyze DNA sequences. |
| 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 |
bio |
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 |
lib |
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.
|
| ucc-cuda |
lib |
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.
This module adds the UCC CUDA support.
|
| ucx |
lib |
Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications
|
| ucx-cuda |
lib |
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. |
| 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. |
| 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. |
| wayland |
vis |
Wayland is a project to define a protocol for a compositor to talk to
its clients as well as a library implementation of the protocol. The
compositor can be a standalone display server running on Linux kernel
modesetting and evdev input devices, an X application, or a wayland
client itself. The clients can be traditional applications, X servers
(rootless or fullscreen) or other display servers.
|
| 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 |
Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets
API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel
and requiring very little (if any) platform specific code. |
| 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. |
| x11 |
vis |
The X Window System (X11) is a windowing system for bitmap displays |
| 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.
|
| xalt |
lib |
XALT 2 is a tool to allow a site to track user executables
and library usage on a cluster. When installed it can tell a site what are
the top executables by Node-Hours or by the number of users or the number
of times it is run. XALT 2 also tracks library usage as well. XALT 2 can
also track package use by R, MATLAB or Python. It tracks both MPI and
non-MPI programs. |
| 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++. |
| xml-compile |
data |
Perl module for compilation based XML processing |
| xml-libxml |
data |
Perl binding for libxml2 |
| xorg-macros |
devel |
X.org macros utilities. |
| xxdiff |
tools |
xxdiff is a graphical file and directories comparator and merge tool. |
| xxhash |
tools |
xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit. |
| 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. |
| yaml-cpp |
tools |
yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec |
| yasm |
lang |
Yasm: Complete rewrite of the NASM assembler with BSD license |
| z3 |
tools |
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. |
