LigerLightweight Iterative Gene set Enrichment in R
Stars: ✭ 44 (-82.26%)
calourexploratory and interactive microbiome analyses based on heatmaps
Stars: ✭ 22 (-91.13%)
WgsimReads simulator
Stars: ✭ 178 (-28.23%)
pathway-mapperPathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Stars: ✭ 47 (-81.05%)
Awesome VdjTools and databases for analyzing HLA and VDJ genes.
Stars: ✭ 43 (-82.66%)
awesome-geneticsA curated list of awesome bioinformatics software.
Stars: ✭ 60 (-75.81%)
ScgenSingle cell perturbation prediction
Stars: ✭ 122 (-50.81%)
block-alignerSIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.
Stars: ✭ 58 (-76.61%)
GatkOfficial code repository for GATK versions 4 and up
Stars: ✭ 1,002 (+304.03%)
crazydocRead DNA sequences from colourful Microsoft Word documents
Stars: ✭ 18 (-92.74%)
CanvasxpressJavaScript VisualizationTools
Stars: ✭ 247 (-0.4%)
chromapFast alignment and preprocessing of chromatin profiles
Stars: ✭ 93 (-62.5%)
UtaUniversal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Stars: ✭ 38 (-84.68%)
reg-genRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Stars: ✭ 64 (-74.19%)
BlacklistApplication for making ENCODE Blacklists
Stars: ✭ 119 (-52.02%)
BioKEENA computational library for learning and evaluating biological knowledge graph embeddings
Stars: ✭ 41 (-83.47%)
EtrfExact Tandem Repeat Finder (not a TRF replacement)
Stars: ✭ 35 (-85.89%)
ccsCCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
Stars: ✭ 79 (-68.15%)
RoaryRapid large-scale prokaryote pan genome analysis
Stars: ✭ 176 (-29.03%)
GenomicDataCommonsProvide R access to the NCI Genomic Data Commons portal.
Stars: ✭ 64 (-74.19%)
BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Stars: ✭ 970 (+291.13%)
bio toolsUseful bioinformatic scripts
Stars: ✭ 35 (-85.89%)
Dna2vecdna2vec: Consistent vector representations of variable-length k-mers
Stars: ✭ 117 (-52.82%)
ngstoolsMy own tools code for NGS data analysis (Next Generation Sequencing)
Stars: ✭ 28 (-88.71%)
FastpAn ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Stars: ✭ 966 (+289.52%)
Cytometry Clustering ComparisonR scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data
Stars: ✭ 30 (-87.9%)
orfipyFast and flexible ORF finder
Stars: ✭ 27 (-89.11%)
Apbs Pdb2pqrAPBS - software for biomolecular electrostatics and solvation
Stars: ✭ 114 (-54.03%)
CATTAn ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.
Stars: ✭ 17 (-93.15%)
RasusaRandomly subsample sequencing reads to a specified coverage
Stars: ✭ 28 (-88.71%)
SVCollectorMethod to optimally select samples for validation and resequencing
Stars: ✭ 20 (-91.94%)
Goleftgoleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Stars: ✭ 175 (-29.44%)
staramrScans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Stars: ✭ 52 (-79.03%)
Sevenbridges RSeven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R
Stars: ✭ 27 (-89.11%)
calN50Compute N50/NG50 and auN/auNG
Stars: ✭ 20 (-91.94%)
FqtoolsAn efficient FASTQ manipulation suite
Stars: ✭ 114 (-54.03%)
CENTIPEDE.tutorial🐛 How to use CENTIPEDE to determine if a transcription factor is bound.
Stars: ✭ 23 (-90.73%)
Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequences
Stars: ✭ 912 (+267.74%)
hotmapWebGL Heatmap Viewer for Big Data and Bioinformatics
Stars: ✭ 13 (-94.76%)
SourmashQuickly search, compare, and analyze genomic and metagenomic data sets.
Stars: ✭ 237 (-4.44%)
CoNekTCoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.
Stars: ✭ 17 (-93.15%)
Uncurl pythonUNCURL is a tool for single cell RNA-seq data analysis.
Stars: ✭ 13 (-94.76%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (-77.82%)
UgeneUGENE is free open-source cross-platform bioinformatics software
Stars: ✭ 112 (-54.84%)
ScispacyA full spaCy pipeline and models for scientific/biomedical documents.
Stars: ✭ 855 (+244.76%)
atroposAn NGS read trimming tool that is specific, sensitive, and speedy. (production)
Stars: ✭ 109 (-56.05%)
AnndataAnnotated data.
Stars: ✭ 171 (-31.05%)
Taxadb🐣 locally query the ncbi taxonomy
Stars: ✭ 26 (-89.52%)
Hap.pyHaplotype VCF comparison tools
Stars: ✭ 249 (+0.4%)
Cyvcf2cython + htslib == fast VCF and BCF processing
Stars: ✭ 243 (-2.02%)
BowtieAn ultrafast memory-efficient short read aligner
Stars: ✭ 221 (-10.89%)
GenometoolsGenomeTools genome analysis system.
Stars: ✭ 186 (-25%)
HifiasmHifiasm: a haplotype-resolved assembler for accurate Hifi reads
Stars: ✭ 134 (-45.97%)
SibeliazA fast whole-genome aligner based on de Bruijn graphs
Stars: ✭ 76 (-69.35%)
Bio.jl[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
Stars: ✭ 257 (+3.63%)