| R |
lang |
R is a free software environment for statistical computing and graphics. |
| 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/
|
| 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. |
| 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. |
| 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 |
| 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. |
| binutils |
tools |
binutils: GNU binary utilities |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| cmake |
devel |
CMake, the cross-platform, open-source build system. CMake is a family of
tools designed to build, test and package software.
|
| comp2comp |
bio |
Comp2Comp is a library for extracting clinical insights from computed tomography scans. |
| ctakes |
data |
Apache cTAKES is a natural language processing system for extraction of information from electronic medical record clinical free-text. |
| 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. |
| 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. |
| eigen |
math |
Eigen is a C++ template library for linear algebra:
matrices, vectors, numerical solvers, and related algorithms. |
| 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. |
| 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. |
| fiji |
tools |
Fiji is an image processing distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. |
| fsl |
data |
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
| 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. |
| 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,...). |
| gd |
bio |
GD.pm - Interface to Gd Graphics Library |
| go |
lang |
Go is an open source programming language that makes it easy to build
simple, reliable, and efficient software. |
| gompi |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit,
including OpenMPI for MPI support. |
| goolf |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain,
including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
| 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. |
| hdf5 |
data |
HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
| 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). |
| htslib |
bio |
A C library for reading/writing high-throughput sequencing data.
This package includes the utilities bgzip and tabix |
| 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.
|
| icu |
lib |
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization
support for software applications. |
| java |
lang |
Java Platform, Standard Edition (Java SE) lets you develop and deploy
Java applications on desktops and servers. |
| jemalloc |
lib |
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and
scalable concurrency support. |
| junit |
devel |
A programmer-oriented testing framework for Java. |
| jupyterlab |
tools |
Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
|
| kallisto |
bio |
Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. |
| knime |
data |
KNIME is an analytics platform for data mining. |
| 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. |
| libiconv |
lib |
Libiconv converts from one character encoding to another through Unicode conversion |
| mamba |
lang |
Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux
(ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands.
|
| 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. |
| matlab |
math |
MATLAB is a high-level language and interactive environment
that enables you to perform computationally intensive tasks faster than with
traditional programming languages such as C, C++, and Fortran. |
| 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. |
| miniforge |
lang |
Miniforge is a free minimal installer for conda and Mamba specific
to conda-forge. |
| 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. |
| 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. |
| 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. |
| ninja |
tools |
Ninja is a small build system with a focus on speed. |
| nodejs |
lang |
Node.js is a platform built on Chrome's JavaScript runtime
for easily building fast, scalable network applications. Node.js uses an
event-driven, non-blocking I/O model that makes it lightweight and efficient,
perfect for data-intensive real-time applications that run across distributed devices. |
| openblas |
numlib |
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
| openmpi |
mpi |
The Open MPI Project is an open source MPI-3 implementation. |
| 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. |
| perl |
lang |
Larry Wall's Practical Extraction and Report Language |
| picard |
bio |
A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| 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. |
| 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.
|
| 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. |
| python |
lang |
Python is a programming language that lets you work
more effectively. |
| rstudio-server |
lang |
RStudio is an integrated development environment (IDE) for the R programming language. |
| salmon |
bio |
Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimates from RNA-seq data. |
| 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. |
| scalapack |
numlib |
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
redesigned for distributed memory MIMD parallel computers. |
| 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++. |
| 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 |
| 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. |
| 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. |
| 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.
|
| ucx |
lib |
Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications
|
| xz |
tools |
xz: XZ utilities |
| yaml-cpp |
tools |
yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec |
| 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. |
