| computational biology |
alphafold |
2.3.1
2.3.2
|
Website |
AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence. |
| computational biology |
alphamissense |
1.0.0
|
Website |
AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence. |
| computational biology |
alphapulldown |
1.0.3
1.0.4
|
Website |
AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. |
| computational biology |
bcl |
3.4.0
|
Website |
The Bio Chemical Library (BCL) is a software package that provides unique tools for biological research, such as protein structure determination from sparse experimental data. |
| computational biology |
calibur |
20120117
|
Website |
Efficient tool for finding structural candidate decoys generated from Ab Initio protein structure prediction methods. |
| computational biology |
colabfold |
2.3.1
|
Website |
AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence. |
| computational biology |
cookhla |
1.0.1
|
Website |
CookHLA is an accurate and efficient HLA imputation method. |
| computational biology |
dssp |
4.4.7
|
Website |
DSSP is an algorithm originally designed by Wolfgang Kabsch and Chris Sander to standardise secondary structure assigment based on atomic coordinates. |
| computational biology |
ensembler |
1.0.5
|
Website |
Software pipeline for automating omics-scale protein modeling and simulation setup. |
| computational biology |
foldx |
4.0
5.0
|
Website |
FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. |
| computational biology |
interproscan |
5.39-77.0
5.50-84.0
|
Website |
Functional analysis of proteins by classifying them into families and predicting domains and important sites. |
| computational biology |
modeller |
10.0
|
Website |
MODELLER is used for homology or comparative modeling of protein three-dimensional structures. |
| computational biology |
msmbuilder |
3.8.0
|
Website |
MSMBuilder is an application and python library. It builds statistical models for high-dimensional time-series. The particular focus of the package is on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. |
| computational biology |
pdbfixer |
1.7.0
|
Website |
The PDBFixer is an easy to use application for fixing problems in Protein Data Bank files |
| computational biology |
phenix |
1.21.2
|
Website |
Python-based Hierarchical ENvironment for Integrated Xtallography. |
| computational biology |
phylip |
3.697
|
Website |
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). |
| computational biology |
rfdiffusion |
1.1.0
|
Website |
RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). |
| cryo-em |
relion |
3.1.3
4.0.2
|
Website |
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a software package that employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination. |
| genomics |
agat |
0.8.0
1.4.0
|
Website |
Suite of tools to handle gene annotations in any GTF/GFF format. |
| genomics |
ampliconarchitect |
1.2
|
Website |
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA. |
| genomics |
analyze_motifs |
1.0
|
Website |
Runs HOMER and kmer enrichment aspects from clip_analysis_legacy to generate useful motif analyses. |
| genomics |
annovar |
042018
25616
29711
|
Website |
ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. |
| genomics |
antismash |
6.0.1
6.1.0
|
Website |
antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. |
| genomics |
anvio |
7
8.0.0
|
Website |
Anvi’o is an open-source, community-driven analysis and visualization platform for microbial ‘omics. |
| genomics |
aracne-ap |
072018
|
Website |
ARACNe-AP (Algorithm for the Reconstruction of Accurate Cellular Networks with Adaptive Partitioning) |
| genomics |
bam-readcount |
0.8.0
|
Website |
Utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. |
| genomics |
bamtools |
2.5.1
|
Website |
C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. |
| genomics |
basemount |
0.15.96
|
Website |
BaseMount is a tool to mount your BaseSpace Sequence Hub data as a Linux file system. |
| genomics |
basespace |
1.3.0
|
Website |
The BaseSpace Sequence Hub CLI supports scripting and programmatic access to BaseSpace Sequence Hub for automation, bulk operations, and other routine functions. |
| genomics |
bbmap |
38.82
39.01
|
Website |
Short read aligner for DNA and RNA-seq data. |
| genomics |
bcftools |
1.11
1.15
1.16
1.19
|
Website |
BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. |
| genomics |
bcftools-mocha |
1.15
|
Website |
BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. |
| genomics |
bcl2fastq2 |
2.2
|
Website |
The Illumina bcl2fastq2 Conversion Software v2.20 demultiplexes sequencing data and converts base call (BCL) files into FASTQ files. |
| genomics |
bedops |
2.4.39
2.4.41
|
Website |
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. |
| genomics |
bedtools2 |
2.25.0
2.30.0
|
Website |
The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. |
| genomics |
bgen |
1.1.7
|
Website |
Reference implementation of the BGEN format, written in C++. |
| genomics |
bicseq2-norm |
0.2.4
|
Website |
BICseq2-norm is for normalizing potential biases in the sequencing data. |
| genomics |
bicseq2-seg |
0.7.2
|
Website |
BICseq2-seg is for detecting CNVs based on the normalized data given by BICseq2-norm. |
| genomics |
bioawk |
1.0
|
Website |
BWK awk modified for biological data |
| genomics |
biobambam2 |
2.0.87
|
Website |
This package contains some tools for processing BAM files. |
| genomics |
biolibc |
0.2.4
|
Website |
Biolibc is a collection of high-quality bricks that can be used to build efficient, robust software applications to replace disposable scripts. Using biolibc, you can easily develop permanent solutions that are easy to use and install, with near-optimal performance, so that no one ever need reinvent that particular wheel. Biolibc also facilitates development of more complex applications by providing many commonly used building blocks, thus releasing you from low-level coding. |
| genomics |
bior |
5.0.0
|
Website |
The Biological Reference Repository (BioR) catalog format is a flexible, readable, indexable, and schema-free format for storing and rapidly accessing arbitrary structured data such as genomic features, diseases, conditions, genetic tests, and drugs. |
| genomics |
bismark |
0.16.3
|
Website |
A tool to map bisulfite converted sequence reads and determine cytosine methylation states. |
| genomics |
blast |
2.9.0
2.12.0
|
Website |
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. |
| genomics |
bowtie |
2.3.4.3
2.5.0
|
Website |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. |
| genomics |
bracken |
2.6.0
2.8.0
|
Website |
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. |
| genomics |
bwa |
0.7.17
|
Website |
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. |
| genomics |
cadd |
1.6
|
Website |
CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. |
| genomics |
canu |
1.8
|
Website |
A single molecule sequence assembler for genomes large and small. |
| genomics |
cava |
1.2.3
|
Website |
CAVA (Clinical Annotation of VAriants) is a lightweight, fast, flexible and easy-to-use Next Generation Sequencing (NGS) variant annotation tool. |
| genomics |
cd-hit |
4.8.1
|
Website |
Program for clustering and comparing protein or nucleotide sequences. |
| genomics |
cellranger |
3.0.0
4.0.0
5.0.1
6.0.0
7.0.0
8.0.0
|
Website |
Set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis |
| genomics |
cellranger-arc |
1.0.1
2.0.1
2.0.2
|
Website |
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 (GEX), chromatin accessibility, and their linkage. |
| genomics |
cellranger-atac |
2.1.0
|
Website |
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 (GEX), chromatin accessibility, and their linkage. |
| genomics |
cellsnp-lite |
1.2.2
|
Website |
cellsnp-lite was initially designed to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo, which assigns cells to donors and detects doublets, even without genotyping reference. |
| genomics |
centrifuge |
1.0.3
|
Website |
Rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. |
| genomics |
circexplorer2 |
2.3.6
|
Website |
CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. |
| genomics |
circlefinder |
1.0
|
Website |
A method to identify Circular DNA (Micro DNA) from pair-end high-throughput sequencing data. |
| genomics |
circlemap |
1.1.4
|
Website |
Circle-Map takes as input an alignment of reads to a reference genome (e.g. a BWA-MEM generated BAM file) and like other methods, it will use those alignments to detect cases were the read has been split into two segments (e.g. split reads) to detect genomic rearrangements supporting a circular DNA structure. |
| genomics |
cite-seq-count |
1.4.4
|
Website |
A tool that allows to get UMI counts from a single cell protein assay. |
| genomics |
clara-parabricks |
4.0.1-1
|
Website |
Nvidia Clara Parabricks is an accelerated compute framework that supports applications across the genomics industry, primarily supporting analytical workflows for DNA, RNA, and somatic mutation detection applications. |
| genomics |
clipper |
2.0.1
|
Website |
CLIPper is a tool to define peaks in your CLIP-seq dataset. |
| genomics |
clustal-omega |
1.2.4
|
Website |
Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. |
| genomics |
cnvkit |
0.9.9
|
Website |
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. |
| genomics |
cobra |
2.0
|
Website |
Containerized Bioinformatics workflow for Reproducible ChIP,ATAC-seq Analysis |
| genomics |
compass |
0.9.10.2
|
Website |
In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes |
| genomics |
concoct |
1.1.0
|
Website |
CONCOCT “bins” metagenomic contigs. Metagenomic binning is the process of clustering sequences into clusters corresponding to operational taxonomic units of some level. |
| genomics |
crossmap |
0.6.6
|
Website |
CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF. |
| genomics |
cufflinks |
2.2.2
|
Website |
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. |
| genomics |
cutadapt |
3.2
3.4
4.0
|
Website |
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. |
| genomics |
cytoscape |
3.9.1
|
Website |
Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. With Cytoscape, you can load molecular and genetic interaction data sets in many standards formats, project and integrate global datasets and functional annotations, establish powerful visual mappings across these data, perform advanced analysis and modeling and visualize and analyze human-curated pathway datasets. |
| genomics |
dapars |
0.9.1
|
Website |
Dynamitic analysis of Alternative PolyAdenylation from RNA-seq |
| genomics |
dcc |
0.5.0
|
Website |
DCC is a python package intended to detect and quantify circRNAs with high specificity. DCC works with the STAR (Dobin et al., 2013) chimeric.out.junction files which contains chimerically aligned reads including circRNA junction spanning reads. |
| genomics |
dcca |
0.0.1
|
Website |
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data. |
| genomics |
dchic |
1.0.0
|
Website |
dcHiC is a tool for differential compartment analysis of Hi-C datasets |
| genomics |
deeptools |
3.5.0
3.5.1
|
Website |
deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. |
| genomics |
depict |
1.194
|
Website |
an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. |
| genomics |
diamond |
0.9.14
|
Website |
DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. |
| genomics |
dram |
1.2.4
|
Website |
DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. |
| genomics |
dropest |
0.8.5
|
Website |
Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements. |
| genomics |
ea-utils |
1.04
|
Website |
Command-line tools for processing biological sequencing data. |
| genomics |
eclipanalyzer |
1.0
|
Website |
This repository contains a series of python based modules to automate the analysis of sequencing data generated from eCLIP (enhanced UV crosslinking and immunoprecipitation) experiments. |
| genomics |
eclipidrmergepeaks |
0.1.0
|
Website |
CWL-defined pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaks. |
| genomics |
eclipregionnormalize |
0.0.4
|
Website |
Pipeline for region-based enrichment. This workflow is defined using CWL v1.0 spec. |
| genomics |
emg-viral-pipeline |
0.3.0
2.0.0
|
Website |
VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. |
| genomics |
enhancer-dissection |
1.0.0
|
Website |
The two programs in this project display variant data, motif data (via highlights). |
| genomics |
ensembl-vep |
103.1
111.0
|
Website |
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. |
| genomics |
esm |
2.0.1
|
Website |
Evolutionary Scale Modeling (esm). Pretrained language models for proteins. |
| genomics |
esmfold |
1.0.3
|
Website |
Evolutionary Scale Modeling (esm). Pretrained language models for proteins. |
| genomics |
express |
1.5.1
|
Website |
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. |
| genomics |
fastq-pair |
1.0
|
Website |
Rewrite paired end fastq files to make sure that all reads have a mate and to separate out singletons.. |
| genomics |
fastq-screen |
0.15.2
|
Website |
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. |
| genomics |
fastqc |
0.11.9
|
Website |
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. |
| genomics |
fastvifi |
1.0
|
Website |
A software to detect viral infection and integration sites for different viruses. FastViFi relies on ViFi and Kraken2 tools. |
| genomics |
fitsne |
1.2.1
|
Website |
FFT-accelerated Interpolation-based t-SNE (FIt-SNE) |
| genomics |
fluxsimulator |
1.2.1
|
Website |
The Flux Simulator aims at modeling RNA-Seq experiments in silico. Sequencing reads are produced from a reference genome according annotated transcripts. |
| genomics |
gatk |
3.8
3.8.1
4.0.11.0
4.1.7.0
4.4.0.0
4.5.0.0
|
Website |
The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. |
| genomics |
gcta |
1.94.1
|
Website |
a tool for Genome-wide Complex Trait Analysis |
| genomics |
gdc-client |
1.6.1
|
Website |
Illumina Array Analysis Platform cli |
| genomics |
geneformer |
0.1.0
|
Website |
Geneformer is a foundation transformer model pretrained on a large-scale corpus of ~30 million single cell transcriptomes to enable context-aware predictions in settings with limited data in network biology. |
| genomics |
genomebrowse |
3.1.0
|
Website |
The free Golden Helix GenomeBrowse tool delivers stunning visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. |
| genomics |
genrich |
0.6.1
|
Website |
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. |
| genomics |
gethomologues |
3.6.1
|
Website |
Get_Homologues is a versatile software package for pan-genome analysis. |
| genomics |
gffcompare |
0.10.1
|
Website |
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). |
| genomics |
gistic |
2.0.23
|
Website |
The GISTIC module identifies regions of the genome that are significantly amplified or deleted across a set of samples. |
| genomics |
glow |
1.1.2
|
Website |
Glow is an open-source toolkit for working with genomic data at biobank-scale and beyond. |
| genomics |
gmap-gsnap |
2016-05-01
2021-12-17
|
Website |
A genomic mapping and alignment program for mRNA and EST sequences. |
| genomics |
gossamer |
1.0.0
|
Website |
Gossamer is an application for doing de novo assembly of high throughput sequencing data. |
| genomics |
gridss |
2.13.2
|
Website |
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. |
| genomics |
hail |
0.2.64
|
Website |
Hail is an open-source library for scalable data exploration and analysis, with a particular emphasis on genomics. |
| genomics |
haslr |
0.8a1
|
Website |
HASLR is a tool for rapid genome assembly of long sequencing reads. |
| genomics |
hicexplorer |
3.7.4
|
Website |
A set of tools for the analysis and visualization of chromosome conformation data |
| genomics |
hisat2 |
2.0.5
2.2.1
|
Website |
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. |
| genomics |
hmmer |
3.3.2
|
Website |
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. |
| genomics |
homer |
4.9.1
4.11.1
5.1
|
Website |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. |
| genomics |
htseq |
0.13.5
|
Website |
HTSeq is a Python package for analysis of high-throughput sequencing data. |
| genomics |
htslib |
1.9
1.10.2
1.11
1.15
1.2
|
Website |
HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. |
| genomics |
humann |
3.0.0a4
3.8
|
Website |
HUMAnN 3.0 is the next generation of HUMAnN (HMP Unified Metabolic Analysis Network). |
| genomics |
iaap-cli |
1.1.0
|
Website |
Illumina Array Analysis Platform cli |
| genomics |
idr |
2.0.2
|
Website |
The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. |
| genomics |
igv |
2.16.2
2.17.4
|
Website |
The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. |
| genomics |
illumina-utils |
2.1
2.11
|
Website |
Software to perform various operations on FASTQ files (such as demultiplexing raw Illumina files, merging partial or complete overlaps, and/or performing quality filtering). |
| genomics |
impute |
2.3.2
|
Website |
IMPUTE version 2 is a genotype imputation and haplotype phasing program. |
| genomics |
impute5 |
1.1.5
|
Website |
IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples. |
| genomics |
jvarkit |
2021.10.13
|
Website |
Java utilities for bioinformatics. |
| genomics |
k2mem |
1.0.0
|
Website |
K2Mem is a variant of Kraken 2 taxonomic sequence classification system that can learn from the previous classifications. |
| genomics |
kaiju |
1.7.2
|
Website |
Kaiju is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. |
| genomics |
kallisto |
0.46.1
|
Website |
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. |
| genomics |
king |
2.1.2
|
Website |
Kinship-based INference for Gwas |
| genomics |
kneaddata |
0.10.0
|
Website |
KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments. |
| genomics |
kobas |
3.0.3
|
Website |
KOBAS (KEGG Orthology-Based Annotation System) is a tool for the annotation of sequences by KEGG Orthology terms. KOBAS also identifies enriched pathways and uses KEGG Pathway, PID, BioCyc, Reactome, Panther and human data from OMIM, KEGG Disease, FunDO, GAD, NHGRI, and GWAS databases. |
| genomics |
kraken2 |
2.1.1
2.1.3
|
Website |
Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. |
| genomics |
krakenuniq |
0.5.8
|
Website |
Metagenomics classifier with unique k-mer counting for more specific results. |
| genomics |
lefse |
1.1.2
|
Website |
None |
| genomics |
lep-map |
3
|
Website |
Lep-MAP3 (LM3) is a novel linkage map construction software suite. |
| genomics |
lumpy |
0.2.13
|
Website |
A probabilistic framework for structural variant discovery. |
| genomics |
macs2 |
2.2.6
|
Website |
Model-based Analysis for ChIP-Seq |
| genomics |
macs3 |
3.0.0
|
Website |
Model-based Analysis for ChIP-Seq |
| genomics |
maftools |
2.10.0
|
Website |
Provides a comprehensive set of functions for processing MAF files and to perform most commonly used analyses in cancer genomics. |
| genomics |
magicblast |
1.5.0
|
Website |
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. |
| genomics |
magma |
1.1
|
Website |
MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis. |
| genomics |
manorm |
1.1.4
|
Website |
A robust model for quantitative comparison of ChIP-Seq data sets. |
| genomics |
megahit |
1.1.1
1.2.9
|
Website |
MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly. |
| genomics |
meme |
5.3.1
5.4.1
|
Website |
The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. |
| genomics |
metagenemark |
3.38
|
Website |
Metagenomic sequences can be analyzed by MetaGeneMark , the program optimized for speed. |
| genomics |
metaphlan |
2.6.0
4.0.0
|
Website |
MetaPhlAn is a computational tool for profiling the composition of microbial communites from metagenomic shotgun sequencing data with species level resolution. |
| genomics |
metilene |
0.2.6
|
Website |
Fast and sensitive detection of differential DNA methylation |
| genomics |
migec |
1.2.9
|
Website |
Molecular Identifier Guided Error Correction pipeline |
| genomics |
minpath |
1.5
|
Website |
MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. |
| genomics |
mira |
4.0.2
|
Website |
MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio. |
| genomics |
mitohpc |
1.0.0
|
Website |
MitoHPC is used for Calling Mitochondrial Homplasmies and Heteroplasmies, Mitochondrial High Performance Caller |
| genomics |
mixcr |
2.1.11
4.1.0
|
Website |
MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. |
| genomics |
mosaik |
0.9.0891
|
Website |
MOSAIK is a reference-guided aligner for next-generation sequencing technologies. |
| genomics |
mtoolbox |
1.2.1
|
Website |
A bioinformatics pipeline to analyze mtDNA from NGS data. |
| genomics |
multiqc |
1.11
1.17
1.18
|
Website |
MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples. |
| genomics |
muscle |
3.8.1551
|
Website |
MUSCLE is widely-used software for making multiple alignments of biological sequences. |
| genomics |
mutsig2cv |
1.0
|
Website |
MutSig2CV analyzes somatic point mutations discovered in DNA sequencing, identifying genes mutated more often than expected by chance given inferred background mutation processes. |
| genomics |
ngmerge |
0.3
|
Website |
Merging paired-end reads and removing sequencing adapters |
| genomics |
octopus |
0.7.4
|
Website |
Haplotype-based variant calling |
| genomics |
oncoimpact |
0.9.4
|
Website |
OncoIMPACT is a first-in-class algorithmic framework that nominates patient-specific driver genes by integratively modeling genomic mutations (point, structural and copy-number) and the resulting perturbations in transcriptional programs via defined molecular networks. |
| genomics |
pacbioapps |
latest
|
Website |
PacBio Secondary Analysis Tools on Bioconda |
| genomics |
parsebiosciences |
1.1.2
|
Website |
Parse's single cell kits facilitate scalable single cell RNA-seq, enabling you to go all the way from samples in a single cell suspension to sequencing data. |
| genomics |
pgap |
2021-07-01
|
Website |
The NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). |
| genomics |
phenolyzer |
0.4.0
|
Website |
Phenolyzer is a software that implements phenotype-based prioritization of candidate genes for human diseases. |
| genomics |
phispy |
4.2.21
|
Website |
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions.. |
| genomics |
picard |
2.6.0
2.25.0
|
Website |
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. |
| genomics |
plink |
1.9.0
2.0.0
|
Website |
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. |
| genomics |
prepareaa |
1.0
|
Website |
A multithread-enabled quickstart tool for AmpliconArchitect. |
| genomics |
prodigal |
2.6.3
|
Website |
Fast, reliable protein-coding gene prediction for prokaryotic genomes. |
| genomics |
prokka |
1.14.6
|
Website |
Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. |
| genomics |
prscs |
1.0.0
|
Website |
PRS-CS is a Python based command line tool that infers posterior SNP effect sizes under continuous shrinkage (CS) priors using GWAS summary statistics and an external LD reference panel. |
| genomics |
prsice2 |
2.3.3
|
Website |
Polygenic Risk Score software. |
| genomics |
pureclip |
1.3.1
|
Website |
PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.. |
| genomics |
pyani |
0.2.12
|
Website |
Application and Python module for whole-genome classification of microbes using Average Nucleotide Identity. |
| genomics |
pyega3 |
4.0.5
|
Website |
The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets. pyEGA3 uses the EGA Data API and has several key features. |
| genomics |
pyscenic |
0.12.1
|
Website |
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data. |
| genomics |
qctool |
2.0.8
|
Website |
QCTOOL is a command-line utility program for manipulation and quality control of gwas datasets and other genome-wide data. |
| genomics |
qiime2 |
2020.11
2024.2
|
Website |
Qiime2 is a next-generation microbiome bioinformatics platform. |
| genomics |
regenie |
3.1.1
|
Website |
regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. |
| genomics |
repeatmasker |
4.1.5
|
Website |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
| genomics |
rgi |
6.0.2
|
Website |
This application is used to predict antibiotic resistome(s) from protein or nucleotide data based on homology and SNP models. |
| genomics |
rhapsody |
0.9.8
|
Website |
Python program, based on ProDy, for pathogenicity prediction of human missense variants. |
| genomics |
rsem |
1.3.3
|
Website |
RSEM RNA-Seq by Expectation-Maximization |
| genomics |
rseqc |
3.0.1
4.0.0
|
Website |
RNA Sequence Quality Control Package |
| genomics |
rvtests |
2.1.0
|
Website |
Rvtests, which stands for Rare Variant tests, is a flexible software package for genetic association analysis for sequence datasets. |
| genomics |
sai-10k-calc |
1.1
|
Website |
Calculator for the prediction of pseudoexonization, intron retention, and exon deletion. |
| genomics |
saige |
1.2.0
|
Website |
SAIGE is an R package developed with Rcpp for genome-wide association tests in large-scale data sets and biobanks. |
| genomics |
salmon |
1.5.2
|
Website |
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. |
| genomics |
sambamba |
0.8.1
|
Website |
Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. |
| genomics |
samblaster |
0.1.26
|
Website |
samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. |
| genomics |
samtools |
1.11
1.15.1
1.2
|
Website |
Samtools is a suite of programs for interacting with high-throughput sequencing data. |
| genomics |
scGPT |
0.1.2
|
Website |
scGPT, a Python package for single-cell multi-omic data analysis using pretrained foundation models. |
| genomics |
scvelo |
0.2.4
|
Website |
scVelo is a scalable toolkit for RNA velocity analysis in single cells, based on Bergen et al. (Nature Biotech, 2020). |
| genomics |
seqkit |
0.15.0
|
Website |
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation |
| genomics |
seqtk |
1.3
|
Website |
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format |
| genomics |
shapeit |
2.904
|
Website |
SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. |
| genomics |
shapeit4 |
4.2.2
|
Website |
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 with multiple key additional features. |
| genomics |
shiftx2 |
1.13
|
Website |
SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input. |
| genomics |
snakemake |
7.3.8
|
Website |
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment. |
| genomics |
snpeff |
4.3
5.2
|
Website |
SnpEff is a variant annotation and effect prediction tool. |
| genomics |
snphylo |
20141127
|
Website |
SNPhylo users can construct a phylogenetic tree from a file containing huge SNP data. |
| genomics |
snptest |
2.5.6
|
Website |
SNPTEST is a program for the analysis of single SNP association in genome-wide studies. |
| genomics |
spaceranger |
1.2.2
1.3.1
2.0.0
2.0.1
2.1.0
|
Website |
Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescnce microscope images. |
| genomics |
spades |
3.15.0
3.15.2
3.15.4
|
Website |
SPAdes is an assembly toolkit containing various assembly pipelines. |
| genomics |
spliceai |
1.3.1
|
Website |
A deep learning-based tool to identify splice variants. |
| genomics |
sratoolkit |
3.0.0
3.0.10
3.1.0
3.1.1
|
Website |
Sequence Read Archive Toolkit(SRA) |
| genomics |
staphb-tk |
1.3.3
|
Website |
The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. |
| genomics |
star |
2.5.2
2.5.3a
2.6.1b
2.7.3a
2.7.9a
2.7.10b
|
Website |
Spliced Transcripts Alignment to a Reference |
| genomics |
star-fusion |
1.10.1
|
Website |
STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. |
| genomics |
stringtie |
2.1.4
|
Website |
High-performance read alignment, quantification and mutation discovery, next-gen sequencing data. |
| genomics |
subread |
2.0.1
2.0.6
|
Website |
High-performance read alignment, quantification and mutation discovery, next-gen sequencing data. |
| genomics |
svaba |
1.1.3
|
Website |
SvABA - Structural variation and indel analysis by assembly. |
| genomics |
taxonkit |
0.14.2
|
Website |
A Practical and Efficient NCBI Taxonomy Toolkit also supports creating NCBI style taxdump files for custom taxonomies. |
| genomics |
tophat |
2.1.1
|
Website |
TopHat is a fast splice junction mapper for RNA-Seq reads. |
| genomics |
trf |
4.09
|
Website |
Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. |
| genomics |
trimgalore |
0.6.6
|
Website |
Trim Galore is a perl wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. |
| genomics |
trimmomatic |
0.38
|
Website |
A flexible read trimming tool for Illumina NGS data |
| genomics |
ucsctools |
1.0
|
Website |
Tools from the UCSC browser. |
| genomics |
umi_tools |
1.1.2
|
Website |
Tools for dealing with Unique Molecular Identifiers |
| genomics |
varscan |
2.4.0
2.4.1
2.4.2
2.4.3
2.4.4
|
Website |
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data. |
| genomics |
varseq |
2.6.1
|
Website |
The free Golden Helix GenomeBrowse tool delivers stunning visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. |
| genomics |
vcf-split |
0.1.5
|
Website |
vcf-split splits a combined-sample VCF stream into single-sample VCF files. |
| genomics |
vcftools |
0.1.16
|
Website |
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. |
| genomics |
velocyto |
0.17
|
Website |
Velocyto is a library for the analysis of RNA velocity. |
| genomics |
vicaller |
1.1
|
Website |
Viral Integration caller (VIcaller) is a bioinformatics tool designed for identifying viral integration events using high-throughput sequencing (HTS) data. |
| genomics |
vifi |
072018
|
Website |
ViFi is a tool for detecting viral integration and fusion mRNA sequences from Next Generation Sequencing data. |
| genomics |
virsorter |
2.2.4
|
Website |
Mining viral signal from microbial genomic data. |
| genomics |
virusseq |
072018
|
Website |
A new algorithmic tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. |
| imaging |
deeplabcutnogui |
2.2
2.3.9
|
Website |
Markerless pose estimation of user-defined features with deep learning for all animals including humans |
| imaging |
mipav |
7.3.0
11.0.3
|
Website |
The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. |
| imaging |
mitograph |
3.0
|
Website |
MitoGraph is a fully automated image processing method and software dedicated to calculating the three-dimensional morphology of mitochondria in live cells. |
| imaging |
monai |
1.3.2
|
Website |
MONAI is a set of open-source, freely availalbe collaborative frameworks built for accelerating research ad clinical collaboration in Medical Imaging. |
| imaging |
openslide |
3.4.1
|
Website |
OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). |
| imaging |
seacr |
1.3
|
Website |
SEACR. Sparse Enrichment Analysis for CUT&RUN |
| molecular dynamics |
gmx_mmpbsa |
1.6.3
|
Website |
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files. |
| neuroimaging |
afni |
16.2.16
19.3.18
21.0.04
22.3.07
24.1.02
|
Website |
AFNI (Analysis of Functional NeuroImages) |
| neuroimaging |
ants |
2.2.0
2.4.0
2.5.2
|
Website |
ANTs is a medical image registration and segmentation toolkit. |
| neuroimaging |
camino |
1.0
|
Website |
Camino is an open-source software toolkit for diffusion MRI processing. |
| neuroimaging |
clara-train-sdk |
1.7.1
|
Website |
NVIDIA Clara Train SDK provides a training framework to help accelerate deep learning training and inference for medical imaging use cases. |
| neuroimaging |
dcm2nii |
122015
|
Website |
dcm2nii is a popular tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the simple NIfTI format used by many scientific tools. |
| neuroimaging |
dcm2niix |
1.0.20210317
1.0.20240327
|
Website |
dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. |
| neuroimaging |
dcmtk |
3.6.1
|
Website |
This DICOM ToolKit (DCMTK) package consists of source code, documentation and installation instructions for a set of software libraries and applications implementing part of the DICOM/MEDICOM Standard. |
| neuroimaging |
dke |
2.6
|
Website |
Diffusional Kurtosis Estimator (DKE) is a software tool for post-processing diffusional kurtosis imaging (DKI) datasets that includes a suite of command-line programs along with a graphical user interface (GUI). |
| neuroimaging |
dsistudio |
latest
|
Website |
DSI Studio is a tractography software tool that maps brain connections and correlates findings with neuropsychological disorders. |
| neuroimaging |
fix |
1.06
|
Website |
FIX attempts to auto-classify ICA components into good vs bad components, so that the bad components can be removed from the 4D FMRI data. |
| neuroimaging |
fmriprep |
20.2.3
21.0.2
22.0.1
22.0.2
|
Website |
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. |
| neuroimaging |
freesurfer |
6.0.0
7.1.0
7.2.0
7.3.2
7.4.1
|
Website |
An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images. |
| neuroimaging |
fsl |
5.0.11
6.0.4.singularity
6.0.4
6.0.7.11
|
Website |
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
| neuroimaging |
fsleyes |
1.1.0
|
Website |
FSLeyes (pronounced fossilise) is the new FSL image viewer for 3D and 4D data (replacing FSLView). It does not perform any processing or analysis of images - that is done by separate tools. |
| neuroimaging |
gradunwarp |
1.2.0
|
Website |
gradunwarp is a Python/Numpy package used to unwarp the distorted volumes (due to the gradient field inhomogenities). |
| neuroimaging |
ismrmrd |
1.0.1
|
Website |
The siemens_to_ismrmrd convertor is used to convert data from Siemens raw data format into ISMRMRD raw data format. |
| neuroimaging |
mne |
0.22.0
|
Website |
Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data; MEG, EEG, sEEG, ECoG, NIRS, and more. |
| neuroimaging |
pyradiomics |
3.0.1
|
Website |
Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks. |
| neuroimaging |
simnibs |
3.2.5
|
Website |
SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation. |
| neuroimaging |
workbench |
1.4.2
2.0.0
|
Website |
Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data |
| population genetics |
eigensoft |
7.2.1
8.0
|
Website |
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). |