PubMed-GitHub

A collection of GitHub repositories that in PubMed abstract.

Top 20 Authors

Rank	Author	Count	Stars	Score
1	brentp	11	2556	81.90
2	lh3	11	2856	77.64
3	ncbi	10	2401	72.76
4	theislab	9	3255	68.10
5	bcgsc	9	1044	59.44
6	OpenGene	6	2398	45.27
7	MolecularAI	6	1320	43.40
8	Illumina	5	1122	37.90
9	marbl	5	1031	36.91
10	broadinstitute	4	2347	32.59
11	rrwick	4	1328	31.91
12	EpistasisLab	3	10556	30.63
13	MannLabs	5	357	30.58
14	choderalab	4	650	28.59
15	nadeemlab	4	402	25.98
16	oxpig	4	372	25.91
17	microsoft	4	350	25.33
18	tanghaibao	3	1490	24.72
19	galaxyproject	3	1617	24.71
20	pachterlab	3	1448	24.45

Note: only count repositories with stars not less than top 1000 threshold (43).

Top 1000 Repositories

CSSEGISandData/COVID-19 (⭐29154 · None) Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE (PMID: 32834919; 33121426; 34248208; 34790453)
kubernetes/charts (⭐15521 · Go) ⚠️(OBSOLETE) Curated applications for Kubernetes (PMID: 30101309)
flairNLP/flair (⭐13637 · Python) A very simple framework for state-of-the-art Natural Language Processing (NLP) (PMID: 33508086)
NVlabs/stylegan2 (⭐10839 · Python) StyleGAN2 - Official TensorFlow Implementation (PMID: 35871688)
EpistasisLab/tpot (⭐9545 · Python) A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming. (PMID: 31165141; 32998684)
pachyderm/pachyderm (⭐6085 · Go) Data-Centric Pipelines and Data Versioning (PMID: 30101309)
tyiannak/pyAudioAnalysis (⭐5716 · Python) Python Audio Analysis Library: Feature Extraction, Classification, Segmentation and Applications (PMID: 26656189)
owid/covid-19-data (⭐5646 · Python) Data on COVID-19 (coronavirus) cases, deaths, hospitalizations, tests • All countries • Updated daily by Our World in Data (PMID: 34610042)
deepchem/deepchem (⭐5209 · Python) Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology (PMID: 28470045)
mdbloice/Augmentor (⭐5037 · Python) Image augmentation library in Python for machine learning. (PMID: 30989173)
google/deepvariant (⭐3100 · Python) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. (PMID: 33399819)
OpenGene/fastp (⭐1801 · C++) An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...) (PMID: 30423086)
theislab/Scanpy (⭐1786 · Python) Single-cell analysis in Python. Scales to >1M cells. (PMID: 29409532)
sokrypton/ColabFold (⭐1766 · Jupyter Notebook) Making Protein folding accessible to all! (PMID: 35637307)
lh3/minimap2 (⭐1707 · C) A versatile pairwise aligner for genomic and spliced nucleotide sequences (PMID: 29750242; 34623391)
broadinstitute/gatk (⭐1621 · Java) Official code repository for GATK versions 4 and up (PMID: 29982281; 31830260)
samtools/samtools (⭐1571 · C) Tools (written in C using htslib) for manipulating next-generation sequencing data (PMID: 24974206)
SmartDataAnalytics/PyKEEN (⭐1552 · Python) 🤖 A Python library for learning and evaluating knowledge graph embeddings (PMID: 30768158)
galaxyproject/galaxy (⭐1328 · Python) Data intensive science for everyone. (PMID: 31197310; 35669346)
shenwei356/seqkit (⭐1222 · Go) A cross-platform and ultrafast toolkit for FASTA/Q file manipulation (PMID: 27706213)
ewels/MultiQC (⭐1182 · JavaScript) Aggregate results from bioinformatics analyses across many samples into a single report. (PMID: 35799367)
glample/tagger (⭐1154 · Python) Named Entity Recognition Tool (PMID: 28881963)
YosefLab/scVI (⭐1145 · Python) Deep probabilistic analysis of single-cell and spatial omics data (PMID: 30504886; 32176273)
fahadshamshad/awesome-transformers-in-medical-imaging (⭐1127 · None) A collection of resources on applications of Transformers in Medical Imaging. (PMID: 37315483)
vlawhern/arl-eegmodels (⭐1090 · Python) This is the Army Research Laboratory (ARL) EEGModels Project: A Collection of Convolutional Neural Network (CNN) models for EEG signal classification, using Keras and Tensorflow (PMID: 29932424)
vgteam/vg (⭐1071 · C++) tools for working with genome variation graphs (PMID: 31406990; 32657356)
ncbi/sra-tools (⭐1060 · C) SRA Tools (PMID: 36698146)
kexinhuang12345/DeepPurpose (⭐929 · Jupyter Notebook) A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics) (PMID: 33275143)
tensorflow/gan (⭐915 · Jupyter Notebook) Tooling for GANs in TensorFlow (PMID: 33381813)
pachterlab/gget (⭐870 · Python) 🧬 gget enables efficient querying of genomic reference databases (PMID: 36610989; 38377393)
jdblischak/workflowr (⭐812 · R) Organize your project into a research website (PMID: 31723427)
InsightSoftwareConsortium/SimpleITK-Notebooks (⭐809 · Jupyter Notebook) Jupyter notebooks for learning how to use SimpleITK (PMID: 29181613)
RainCloudPlots/RainCloudPlots (⭐803 · HTML) Code and tutorials to visualise your data that is both beautiful and statistically valid (PMID: 31069261)
EpistasisLab/pmlb (⭐789 · Python) PMLB: A large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. (PMID: 34677586)
molecularsets/moses (⭐788 · Python) Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models (PMID: 33390943)
arose/nglview (⭐780 · Jupyter Notebook) Jupyter widget to interactively view molecular structures and trajectories (PMID: 29236954)
tanghaibao/goatools (⭐734 · Python) Python library to handle Gene Ontology (GO) terms (PMID: 30022098)
deeptools/pyGenomeTracks (⭐729 · Python) python module to plot beautiful and highly customizable genome browser tracks (PMID: 32745185)
MrGiovanni/ModelsGenesis (⭐723 · Jupyter Notebook) [MICCAI 2019] [MEDIA 2020] Models Genesis (PMID: 32766570; 33188996)
tanghaibao/jcvi (⭐702 · Python) Python library to facilitate genome assembly, annotation, and comparative genomics (PMID: 25583564)
volkamerlab/TeachOpenCADD (⭐693 · Jupyter Notebook) TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data (PMID: 30963287)
awslabs/dgl-lifesci (⭐690 · Python) Python package for graph neural networks in chemistry and biology (PMID: 34693143)
taoliu/MACS (⭐687 · Cython) MACS -- Model-based Analysis of ChIP-Seq (PMID: 24743991)
ablab/spades (⭐686 · C++) SPAdes Genome Assembler (PMID: 31510642; 32413137)
brentp/mosdepth (⭐664 · Nim) fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing (PMID: 29096012)
beoutbreakprepared/nCoV2019 (⭐659 · HTML) Location for summaries and analysis of data related to n-CoV 2019, first reported in Wuhan, China (PMID: 33051749)
arose/ngl (⭐652 · TypeScript) WebGL protein viewer (PMID: 29850778)
torognes/vsearch (⭐636 · C++) Versatile open-source tool for microbiome analysis (PMID: 27781170)
NeuroTechX/moabb (⭐635 · Python) Mother of All BCI Benchmarks (PMID: 30177583)
davidemms/OrthoFinder (⭐635 · Python) Phylogenetic orthology inference for comparative genomics (PMID: 31727128)
naver/biobert-pretrained (⭐634 · None) BioBERT: a pre-trained biomedical language representation model for biomedical text mining (PMID: 31501885)
samtools/BCFtools (⭐623 · C) This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html (PMID: 26826718)
igvteam/igv (⭐615 · Java) Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations (PMID: 36562559)
molstar/molstar (⭐596 · TypeScript) A comprehensive macromolecular library (PMID: 34864908)
ZhaoZhibin/DL-based-Intelligent-Diagnosis-Benchmark (⭐585 · Python) Source codes for the paper "Deep Learning Algorithms for Rotating Machinery Intelligent Diagnosis: An Open Source Benchmark Study" (PMID: 32854956)
biojava/biojava (⭐581 · Java) 📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data. (PMID: 25505094; 28334105; 30735498)
KlugerLab/FIt-SNE (⭐580 · C++) Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE) (PMID: 30742040)
ialbert/biostar-central (⭐574 · Python) Biostar Q&A (PMID: 32640986)
rrwick/Bandage (⭐565 · C++) a Bioinformatics Application for Navigating De novo Assembly Graphs Easily (PMID: 26099265)
gnina/gnina (⭐562 · C++) A deep learning framework for molecular docking (PMID: 34108002)
YichiZhang98/SAM4MIS (⭐561 · None) Segment Anything Model for Medical Image Segmentation: paper list and open-source project summary (PMID: 38422961)
ThomasYeoLab/CBIG (⭐560 · MATLAB) None (PMID: 28981612; 29770530; 30974241; 31229658; 33942058; 36918136)
broadinstitute/keras-rcnn (⭐551 · Python) Keras package for region-based convolutional neural networks (RCNNs) (PMID: 32652926)
jerryji1993/DNABERT (⭐549 · Python) DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome (PMID: 33538820)
MolecularAI/aizynthfinder (⭐546 · Python) A tool for retrosynthetic planning (PMID: 34342428; 38778382)
owkin/PyDESeq2 (⭐532 · Python) A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA. (PMID: 37669147)
rrwick/Unicycler (⭐530 · C++) hybrid assembly pipeline for bacterial genomes (PMID: 28594827)
pachterlab/ffq (⭐528 · Python) A tool to find sequencing data and metadata from public databases. (PMID: 36610997)
CERN/TIGRE (⭐520 · MATLAB) TIGRE: Tomographic Iterative GPU-based Reconstruction Toolbox (PMID: 36088800)
HazyResearch/hyena-dna (⭐518 · Assembly) Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena (PMID: 37426456)
fritzsedlazeck/Sniffles (⭐518 · Python) Structural variation caller using third generation sequencing (PMID: 28456410; 29713083)
skovaka/UNCALLED (⭐514 · C++) Raw nanopore signal mapper that enables real-time targeted sequencing (PMID: 33257863)
theislab/anndata (⭐511 · Python) Annotated data. (PMID: 29409532)
soedinglab/hh-suite (⭐508 · C) Remote protein homology detection suite. (PMID: 31521110)
zqfang/GSEApy (⭐508 · Python) Gene Set Enrichment Analysis in Python (PMID: 36426870)
gamcil/clinker (⭐505 · Python) Gene cluster comparison figure generator (PMID: 33459763)
etal/cnvkit (⭐498 · Python) Copy number variant detection from targeted DNA sequencing (PMID: 27100738)
immunogenomics/harmony (⭐497 · R) Fast, sensitive and accurate integration of single-cell data with Harmony (PMID: 31740819)
ruanjue/wtdbg2 (⭐497 · C) Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly (PMID: 31819265)
ryanlayer/samplot (⭐492 · Python) Plot structural variant signals from many BAMs and CRAMs (PMID: 34034781)
Martinsos/edlib (⭐488 · C++) Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. (PMID: 28453688)
biojs/biojs (⭐484 · None) 🔬A library of JavaScript components to represent biological data (PMID: 24627804; 24715980; 24741440; 24860644; 25075287; 25075288; 25075290)
ncoudray/DeepPATH (⭐484 · Python) Classification of Lung cancer slide images using deep-learning (PMID: 30224757)
Ildaron/ironbci (⭐479 · C) Open-Source Brain-Computer Interface, ADS1299 and STM32 (PMID: 34586477)
BMIRDS/deepslide (⭐476 · Python) Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images. (PMID: 30833650)
lindenb/jvarkit (⭐468 · Java) Java utilities for Bioinformatics (PMID: 29186339)
OpenMS/OpenMS (⭐463 · C++) The codebase of the OpenMS project (PMID: 25927999)
seqan/seqan (⭐458 · C++) SeqAn's official repository. (PMID: 29232861)
benjjneb/dada2 (⭐455 · R) Accurate sample inference from amplicon data with single nucleotide resolution (PMID: 27214047)
ecogenomics/gtdbtk (⭐444 · Python) GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. (PMID: 31730192; 36218463)
saeyslab/nichenetr (⭐442 · R) NicheNet: predict active ligand-target links between interacting cells (PMID: 31819264)
aiqm/torchani (⭐435 · Python) Accurate Neural Network Potential on PyTorch (PMID: 32568524)
OpenGVLab/VideoMAEv2 (⭐430 · Python) [CVPR 2023] VideoMAE V2: Scaling Video Masked Autoencoders with Dual Masking (PMID: 38600138)
pezmaster31/bamtools (⭐410 · C++) C++ API & command-line toolkit for working with BAM data (PMID: 23620359)
omnideconv/immunedeconv (⭐408 · R) A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods (PMID: 38464974)
aristoteleo/dynamo-release (⭐405 · Python) Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses (PMID: 35108499)
oschwengers/bakta (⭐404 · Python) Rapid & standardized annotation of bacterial genomes, MAGs & plasmids (PMID: 34739369)
oddt/oddt (⭐400 · Python) Open Drug Discovery Toolkit (PMID: 26101548; 30202917)
agshumate/Liftoff (⭐398 · Python) An accurate GFF3/GTF lift over pipeline (PMID: 33320174)
prody/ProDy (⭐396 · Python) A Python Package for Protein Dynamics Analysis (PMID: 33822884; 34240100)
Illumina/manta (⭐388 · C++) Structural variant and indel caller for mapped sequencing data (PMID: 26647377)
marbl/mash (⭐377 · C++) Fast genome and metagenome distance estimation using MinHash (PMID: 27323842)
cabani/MaskedFace-Net (⭐372 · None) MaskedFace-Net is a dataset of human faces with a correctly and incorrectly worn mask based on the dataset Flickr-Faces-HQ (FFHQ). (PMID: 33521223)
bxlab/metaWRAP (⭐371 · Shell) MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis (PMID: 30219103)
nservant/HiC-Pro (⭐370 · Python) HiC-Pro: An optimized and flexible pipeline for Hi-C data processing (PMID: 26619908)
digitalmethodsinitiative/dmi-tcat (⭐366 · PHP) Digital Methods Initiative - Twitter Capture and Analysis Toolset (PMID: 33665150)
haddocking/pdb-tools (⭐366 · Python) A dependency-free cross-platform swiss army knife for PDB files. (PMID: 30705752)
amkozlov/raxml-ng (⭐364 · C++) RAxML Next Generation: faster, easier-to-use and more flexible (PMID: 31070718; 31755898)
lishen/end2end-all-conv (⭐360 · Jupyter Notebook) Deep Learning to Improve Breast Cancer Detection on Screening Mammography (PMID: 31467326)
brentp/cyvcf2 (⭐359 · Cython) cython + htslib == fast VCF and BCF processing (PMID: 28165109)
ncbi/GeneGPT (⭐358 · Python) Code and data for GeneGPT. (PMID: 38341654)
wmayner/pyphi (⭐358 · Python) A toolbox for integrated information theory. (PMID: 30048445)
fbreitwieser/pavian (⭐356 · R) 🌈 Interactive analysis of metagenomics data (PMID: 31553437)
mlpen/Nystromformer (⭐351 · Python) None (PMID: 34745767)
Illumina/strelka (⭐350 · C++) Strelka2 germline and somatic small variant caller (PMID: 30013048)
brentp/vcfanno (⭐350 · Go) annotate a VCF with other VCFs/BEDs/tabixed files (PMID: 27250555)
gpertea/gffread (⭐350 · C++) GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more (PMID: 32489650)
pastas/pastas (⭐349 · Python) Pastas is an open-source Python framework for the analysis of groundwater time series. (PMID: 31347164)
gpertea/stringtie (⭐348 · C++) Transcript assembly and quantification for RNA-Seq (PMID: 35648784)
jtamames/SqueezeMeta (⭐343 · C) A complete pipeline for metagenomic analysis (PMID: 30733714)
kqwang/phase-recovery (⭐343 · None) Resources for phase recovery (also called phase imaging, phase retrieval, or phase reconstruction) (PMID: 38161203)
MolecularAI/Reinvent (⭐332 · Python) None (PMID: 33118816)
TissueImageAnalytics/tiatoolbox (⭐330 · Python) Computational Pathology Toolbox developed by TIA Centre, University of Warwick. (PMID: 35640384)
BBillot/SynthSeg (⭐324 · Python) Contrast-agnostic segmentation of MRI scans (PMID: 34367472)
dstahlke/gnuplot-iostream (⭐324 · C++) C++ interface to gnuplot (PMID: 27402903)
taozh2017/RGBD-SODsurvey (⭐322 · MATLAB) RGB-D Salient Object Detection: A Survey (PMID: 33432275)
beringresearch/ivis (⭐319 · Python) Dimensionality reduction in very large datasets using Siamese Networks (PMID: 31222035)
stamatak/standard-RAxML (⭐316 · C) None (PMID: 34410861; 37337442)
jonathanking/sidechainnet (⭐314 · Python) An all-atom protein structure dataset for machine learning. (PMID: 34213059)
oushujun/EDTA (⭐312 · Perl) Extensive de-novo TE Annotator (PMID: 31843001; 33900591)
MarioniLab/miloR (⭐311 · R) R package implementation of Milo for testing for differential abundance in KNN graphs (PMID: 34594043)
whatshap/whatshap (⭐310 · Python) Read-based phasing of genomic variants, also called haplotype assembly (PMID: 29949989; 37928341)
arq5x/lumpy-sv (⭐301 · C) lumpy: a general probabilistic framework for structural variant discovery (PMID: 24970577)
bcgsc/abyss (⭐300 · C++) 🔬 Assemble large genomes using short reads (PMID: 26209068; 35729491)
williamgilpin/pypdb (⭐300 · Python) A Python API for the RCSB Protein Data Bank (PDB) (PMID: 26369703)
saketkc/pysradb (⭐297 · Python) Package for fetching metadata and downloading data from SRA/ENA/GEO (PMID: 31114675)
imagej/imglib (⭐292 · Java) A generic next-generation Java library for image processing (PMID: 22962343)
lh3/miniasm (⭐291 · TeX) Ultrafast de novo assembly for long noisy reads (though having no consensus step) (PMID: 27153593)
mengyao/Complete-Striped-Smith-Waterman-Library (⭐287 · C) None (PMID: 24324759)
ncbi/pgap (⭐287 · Common Workflow Language) NCBI Prokaryotic Genome Annotation Pipeline (PMID: 37962425)
philres/ngmlr (⭐285 · C++) NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations (PMID: 29713083)
torchmd/torchmd-net (⭐284 · Python) Neural network potentials (PMID: 38463504; 38743033)
usnistgov/jarvis (⭐281 · Python) JARVIS-Tools: an open-source software package for data-driven atomistic materials design. Publications: https://scholar.google.com/citations?user=3w6ej94AAAAJ (PMID: 30117438; 32165788; 32165790; 33850146)
PhanstielLab/plotgardener (⭐276 · R) None (PMID: 35134826)
uncbiag/registration (⭐270 · TeX) Image Registration (PMID: 32523327; 36081637)
dmcable/RCTD (⭐267 · HTML) Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics (PMID: 33603203)
dmcable/spacexr (⭐267 · HTML) Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics (PMID: 36050488)
schneebergerlab/plotsr (⭐265 · Python) Tool to plot synteny and structural rearrangements between genomes (PMID: 35561173)
spglib/spglib (⭐264 · C) C library for finding and handling crystal symmetries (PMID: 37668050)
hafen/trelliscopejs (⭐262 · R) TrelliscopeJS R Package (PMID: 36622218)
marbl/MashMap (⭐259 · C++) A fast approximate aligner for long DNA sequences (PMID: 30423094; 37603771)
brentp/somalier (⭐254 · Nim) fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy" (PMID: 32664994)
marianattestad/ribbon (⭐251 · JavaScript) A genome browser that shows long reads and complex variants better (PMID: 32766814)
jtextor/dagitty (⭐248 · JavaScript) Graphical analysis of structural causal models / graphical causal models. (PMID: 28089956)
theislab/scgen (⭐248 · Python) Single cell perturbation prediction (PMID: 31363220)
maickrau/GraphAligner (⭐247 · C++) None (PMID: 30851095; 32972461)
Kinggerm/GetOrganelle (⭐246 · Python) Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS) (PMID: 32912315)
brentp/slivar (⭐246 · Nim) genetic variant expressions, annotation, and filtering for great good. (PMID: 34267211)
sigven/pcgr (⭐246 · R) Personal Cancer Genome Reporter (PCGR) (PMID: 29272339)
tSchlegl/f-AnoGAN (⭐245 · Python) Code for reproducing f-AnoGAN training and anomaly scoring (PMID: 30831356)
lmdu/pyfastx (⭐241 · C) a python package for fast random access to sequences from plain and gzipped FASTA/Q files (PMID: 33341884)
MolecularAI/REINVENT4 (⭐239 · Python) AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization. (PMID: 38383444)
gtonkinhill/panaroo (⭐239 · Python) An updated pipeline for pangenome investigation (PMID: 32698896)
lukasturcani/stk (⭐239 · Python) A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases. (PMID: 34240979)
opencobra/cobratoolbox (⭐238 · MATLAB) The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation: (PMID: 27993782; 28158334; 30052768; 37697651)
jeffdaily/parasail (⭐236 · C) Pairwise Sequence Alignment Library (PMID: 26864881)
schatzlab/genomescope (⭐236 · JavaScript) Fast genome analysis from unassembled short reads (PMID: 28369201)
tjiangHIT/cuteSV (⭐234 · Python) Long read based human genomic structural variation detection with cuteSV (PMID: 32746918; 35751813)
taowenmicro/EasyMicrobiomeR (⭐233 · HTML) Using R language in microbiome analysis (PMID: 37128855)
alekseyzimin/masurca (⭐232 · M4) None (PMID: 35120119)
biocommons/hgvs (⭐232 · Python) Python library to parse, format, validate, normalize, and map sequence variants. pip install hgvs (PMID: 28967166)
smirarab/ASTRAL (⭐228 · Java) Accurate Species TRee ALgorithm (PMID: 25161245; 26072508; 30903685)
RasmussenLab/vamb (⭐227 · Python) Variational autoencoder for metagenomic binning (PMID: 33398153)
adamewing/bamsurgeon (⭐227 · Python) tools for adding mutations to existing .bam files, used for testing mutation callers (PMID: 25984700; 30400818)
marbl/winnowmap (⭐227 · C) Long read / genome alignment software (PMID: 32657365)
rdk/p2rank (⭐227 · Groovy) P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure. (PMID: 31114880)
dasmoth/dalliance (⭐226 · JavaScript) Interactive web-based genome browser. (PMID: 26315906)
qiicr/dcmqi (⭐225 · C++) dcmqi (DICOM for Quantitative Imaging) is a free, open source C++ library for conversion between imaging research formats and the standard DICOM representation for image analysis results (PMID: 29092948)
ssadedin/bpipe (⭐225 · Groovy) Bpipe - a tool for running and managing bioinformatics pipelines (PMID: 26460497)
EpistasisLab/Aliro (⭐222 · JavaScript) Aliro: AI-Driven Data Science (PMID: 37796839)
choderalab/pymbar (⭐222 · Python) Python implementation of the multistate Bennett acceptance ratio (MBAR) (PMID: 25808134)
RGLab/MAST (⭐221 · R) Tools and methods for analysis of single cell assay data in R (PMID: 26653891)
xiangyue9607/BioNEV (⭐221 · Python) Graph Embedding Evaluation / Code and Datasets for "Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations" (Bioinformatics 2020) (PMID: 31584634)
labgem/PPanGGOLiN (⭐217 · Python) Build a partitioned pangenome graph from microbial genomes (PMID: 32191703; 33381850)
ryanlayer/giggle (⭐217 · C) Interval data structure (PMID: 29309061)
KamilSJaron/smudgeplot (⭐216 · R) Inference of ploidy and heterozygosity structure using whole genome sequencing data (PMID: 32188846)
bcgsc/NanoSim (⭐215 · Python) Nanopore sequence read simulator (PMID: 32520350; 36939007)
fbreitwieser/krakenuniq (⭐215 · C++) 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results (PMID: 30445993)
iqtree/iqtree2 (⭐215 · C++) NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org (PMID: 36383168; 37656933)
debbiemarkslab/evcouplings (⭐213 · Jupyter Notebook) Evolutionary couplings from protein and RNA sequence alignments (PMID: 30304492)
hkmztrk/DeepDTA (⭐213 · Python) None (PMID: 30423097)
GregoryFaust/samblaster (⭐212 · C++) samblaster: a tool to mark duplicates and extract discordant and split reads from sam files. (PMID: 24812344)
cambridgeltl/MTL-Bioinformatics-2016 (⭐211 · Python) None (PMID: 32415963)
INCATools/ontology-development-kit (⭐210 · Jinja) Bootstrap an OBO Library ontology (PMID: 36208225)
ucscGenomeBrowser/kent (⭐209 · C) UCSC Genome Browser source tree. Stable branch: "beta". (PMID: 28108446)
brentp/goleft (⭐208 · Go) goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary (PMID: 29048539)
HajkD/biomartr (⭐206 · R) Genomic Data Retrieval with R (PMID: 28110292)
ZJUFanLab/scCATCH (⭐205 · R) Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data (PMID: 32062421)
PacificBiosciences/FALCON (⭐204 · Python) FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries (PMID: 27749838)
showteeth/ggcoverage (⭐204 · R) Visualize and annotate genomic coverage with ggplot2 (PMID: 37559015)
griffithlab/GenVisR (⭐203 · R) Genome data visualizations (PMID: 27288499)
jeetsukumaran/DendroPy (⭐203 · Python) A Python library for phylogenetic scripting, simulation, data processing and manipulation. (PMID: 20421198)
CapsuleEndoscope/EndoSLAM (⭐202 · Python) EndoSLAM Dataset and an Unsupervised Monocular Visual Odometry and Depth Estimation Approach for Endoscopic Videos: Endo-SfMLearner (PMID: 33930829)
choderalab/espaloma (⭐202 · Python) Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196 (PMID: 36349096)
thinng/GraphDTA (⭐201 · Python) GraphDTA: Predicting drug-target binding affinity with graph neural networks (PMID: 33119053)
noriakis/ggkegg (⭐199 · R) Analyzing and visualizing KEGG information using the grammar of graphics (PMID: 37846038)
shervinea/enzynet (⭐199 · Python) EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation (PMID: 29740518)
TGAC/KAT (⭐198 · C++) The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra. (PMID: 27797770)
anjany/verse (⭐198 · Jupyter Notebook) Everything about the 'Large Scale Vertebrae Segmentation Challenge' @ MICCAI 2019-2020 (PMID: 34340104)
wdecoster/nanopack (⭐198 · Python) An overview of all nanopack tools (PMID: 29547981; 37171891)
wyp1125/MCScanX (⭐198 · CAP CDS) MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world! (PMID: 38491145)
kormilitzin/med7 (⭐197 · None) None (PMID: 34412834)
SajadMo/SleepEEGNet (⭐195 · Python) SleepEEGNet: Automated Sleep Stage Scoring with Sequence to Sequence Deep Learning Approach (PMID: 31063501)
pmelsted/bifrost (⭐195 · C++) Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs (PMID: 32943081)
Nextomics/NextPolish (⭐194 · None) Fast and accurately polish the genome generated by long reads. (PMID: 31778144)
dariober/ASCIIGenome (⭐194 · Java) Text Only Genome Viewer! (PMID: 28119307)
AstrobioMike/GToTree (⭐192 · Shell) A user-friendly workflow for phylogenomics (PMID: 30865266)
rdkit/mmpdb (⭐192 · Python) A package to identify matched molecular pairs and use them to predict property changes. (PMID: 29770697)
vibansal/HapCUT2 (⭐192 · C) software tools for haplotype assembly from sequence data (PMID: 36335497)
mirnylab/cooler (⭐191 · Python) A cool place to store your Hi-C (PMID: 31290943; 33135074)
atks/vt (⭐190 · C) A tool set for short variant discovery in genetic sequence data. (PMID: 25701572)
mortazavilab/PyWGCNA (⭐190 · Jupyter Notebook) PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA) (PMID: 37399090)
cerr/CERR (⭐188 · MATLAB) Matlab/Octave based platform for Radiological Research. (PMID: 34874302)
theislab/paga (⭐188 · Jupyter Notebook) Mapping out the coarse-grained connectivity structures of complex manifolds. (PMID: 30890159)
debbiemarkslab/DeepSequence (⭐187 · Python) A generative latent variable model for biological sequence families. (PMID: 30250057)
danmcduff/iphys-toolbox (⭐186 · MATLAB) A MATLAB toolbox for iPPG analysis. The toolbox includes implementations of commonly used methods. (PMID: 31947335)
vsbuffalo/scidataflow (⭐185 · Rust) Command line scientific data management tool (PMID: 38180848)
ChiLiubio/microeco (⭐180 · R) An R package for data analysis in microbial community ecology (PMID: 33332530)
gpertea/gffcompare (⭐180 · C++) classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF (PMID: 32489650)
openvax/mhcflurry (⭐180 · Python) Peptide-MHC I binding affinity prediction (PMID: 32124315; 32711842)
pangenome/odgi (⭐180 · C++) Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs (PMID: 35552372)
privefl/bigsnpr (⭐180 · R) R package for the analysis of massive SNP arrays. (PMID: 32415959)
isovic/graphmap (⭐177 · C++) GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here: (PMID: 27079541)
alanwilter/acpype (⭐174 · Python) OFFICIAL: AnteChamber PYthon Parser interfacE (PMID: 37252824)
choderalab/perses (⭐174 · Python) Experiments with expanded ensembles to explore chemical space (PMID: 37450482)
ekimb/rust-mdbg (⭐174 · Rust) minimizer-space de Bruijn graphs (mdBG) for whole genome assembly (PMID: 34525345)
franciscozorrilla/metaGEM (⭐174 · Python) 💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data (PMID: 34614189)
HadrienG/InSilicoSeq (⭐173 · Python) 🚀 A sequencing simulator (PMID: 30016412)
Illumina/ExpansionHunter (⭐173 · C++) A tool for estimating repeat sizes (PMID: 31134279)
shenwei356/kmcp (⭐173 · Go) Accurate metagenomic profiling && Fast large-scale sequence/genome searching (PMID: 36579886)
KristapsE/DP4-AI (⭐172 · Python) Python workflow for DP5 and DP4 analysis of organic molecules (PMID: 34122893)
aquaskyline/Clairvoyante (⭐172 · Python) Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing (PMID: 30824707)
soedinglab/metaeuk (⭐172 · C) MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics (PMID: 32245390)
machinegun/SALSA (⭐171 · Python) SALSA: A tool to scaffold long read assemblies with Hi-C data (PMID: 31433799)
Genetalks/gtz (⭐170 · None) A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks. (PMID: 29297296)
bjornwallner/DockQ (⭐170 · Python) DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol (PMID: 27560519)
vgteam/sequenceTubeMap (⭐170 · JavaScript) displays multiple genomic sequences in the form of a tube map (PMID: 31368484)
alexanderkroner/saliency (⭐169 · Python) Contextual Encoder-Decoder Network for Visual Saliency Prediction [Neural Networks 2020] (PMID: 32563023)
kexinhuang12345/moltrans (⭐169 · Jupyter Notebook) MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics) (PMID: 33070179)
Superzchen/iFeature (⭐168 · Python) iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates five kinds of frequently used feature clustering algorithms, four feature selection algorithms and three dimensionality reduction algorithms. (PMID: 29528364)
jbkinney/logomaker (⭐168 · Jupyter Notebook) Software for the visualization of sequence-function relationships (PMID: 31821414)
malonge/RaGOO (⭐167 · Python) RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag (PMID: 31661016)
molgenis/systemsgenetics (⭐167 · Java) Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool (PMID: 32532224; 34792549)
ndierckx/NOVOPlasty (⭐167 · Perl) NOVOPlasty - The organelle assembler and heteroplasmy caller (PMID: 28204566; 33575563)
stephaneguindon/phyml (⭐166 · C) PhyML -- Phylogenetic estimation using (Maximum) Likelihood (PMID: 30977781)
XinhaoLi74/SmilesPE (⭐165 · Jupyter Notebook) SMILES Pair Encoding: A data-driven substructure representation of chemicals (PMID: 33715361)
saezlab/decoupleR (⭐165 · R) R package to infer biological activities from omics data using a collection of methods. (PMID: 36699385)
yiluheihei/microbiomeMarker (⭐165 · R) R package for microbiome biomarker discovery (PMID: 35771644)
abyzovlab/CNVpytor (⭐163 · Python) a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads (PMID: 34817058)
baoe/AlignGraph (⭐163 · C++) Algorithm for secondary de novo genome assembly guided by closely related references (PMID: 24932000)
mkirsche/Jasmine (⭐163 · Java) Jasmine: SV Merging Across Samples (PMID: 36658279)
open2c/bioframe (⭐163 · Python) Genomic Interval Operations on Pandas DataFrames (PMID: 38402507)
huangnengCSU/compleasm (⭐162 · Python) A genome completeness evaluation tool based on miniprot (PMID: 37758247)
sorgerlab/indra (⭐162 · Python) INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models. (PMID: 31070726)
galaxyproject/tools-iuc (⭐161 · HTML) Tool Shed repositories maintained by the Intergalactic Utilities Commission (PMID: 34096994)
herrmannlab/highdicom (⭐161 · Python) High-level DICOM abstractions for the Python programming language (PMID: 35995898)
AnantharamanLab/METABOLIC (⭐160 · Perl) A scalable high-throughput metabolic and biogeochemical functional trait profiler (PMID: 35172890)
neurodata/neuroparc (⭐160 · Jupyter Notebook) None (PMID: 33686079)
BaselAbujamous/clust (⭐159 · Python) Automatic and optimised consensus clustering of one or more heterogeneous datasets (PMID: 30359297)
UCLCheminformatics/ScaffoldGraph (⭐159 · Python) ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees. (PMID: 32232438)
chrisamiller/fishplot (⭐159 · R) Create timecourse "fish plots" that show changes in the clonal architecture of tumors (PMID: 27821060)
dnbaker/dashing (⭐159 · C++) Fast and accurate genomic distances using HyperLogLog (PMID: 31801633)
nickabattista/IB2d (⭐159 · MATLAB) An easy to use immersed boundary method in 2D, with full implementations in MATLAB and Python that contains over 75 built-in examples, including multiple options for fiber-structure models and advection-diffusion, Boussinesq approximations, and/or artificial forcing. (PMID: 28355146)
bjing2016/EigenFold (⭐158 · Jupyter Notebook) EigenFold: Generative Protein Structure Prediction with Diffusion Models (PMID: 37064532)
divelab/MoleculeX (⭐158 · Python) None (PMID: 35179547)
marcelauliano/MitoHiFi (⭐158 · Python) Find, circularise and annotate mitogenome from PacBio assemblies (PMID: 37464285)
duartegroup/autodE (⭐157 · Python) automated reaction profile generation (PMID: 33108028)
mfumagalli/ngsTools (⭐157 · R) Programs to analyse NGS data for population genetics purposes (PMID: 24458950)
pymzML/pymzML (⭐156 · Python) pymzML - an interface between Python and mzML Mass spectrometry Files (PMID: 29394323)
brentp/hts-nim (⭐154 · Nim) nim wrapper for htslib for parsing genomics data files (PMID: 29718142)
millanek/Dsuite (⭐154 · C++) Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species (PMID: 33012121)
patrickbryant1/Umol (⭐154 · Jupyter Notebook) Protein-ligand structure prediction (PMID: 38806453)
ComparativeGenomicsToolkit/hal (⭐153 · C++) Hierarchical Alignment Format (PMID: 32463100)
dsehnal/LiteMol (⭐153 · JavaScript) A library/plugin for handling 3D structural molecular data (not only) in the browser. (PMID: 30179493)
glennhickey/hal (⭐153 · C++) Hierarchical Alignment Format (PMID: 23505295)
nygenome/lancet (⭐153 · C) Microassembly based somatic variant caller for NGS data (PMID: 30271907; 33241313)
smarco/WFA (⭐153 · C) WFA-lib: Wavefront alignment algorithm library v2 (PMID: 32915952)
BenevolentAI/DeeplyTough (⭐151 · Python) DeeplyTough: Learning Structural Comparison of Protein Binding Sites (PMID: 32023053)
crsl4/PhyloNetworks (⭐150 · Julia) A Julia package for statistical inference, data manipulation and visualization of phylogenetic networks (PMID: 28961984)
molML/MoleculeACE (⭐150 · Python) A tool for evaluating the predictive performance on activity cliff compounds of machine learning models (PMID: 36456532)
venyao/shinyCircos (⭐150 · HTML) an R/shiny application for creation of Circos plot interactively (PMID: 29186362)
divonlan/genozip (⭐149 · C) A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too (PMID: 32407471)
statgen/locuszoom (⭐149 · JavaScript) A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. (PMID: 33734315)
KorfLab/StochHMM (⭐148 · C++) A Hidden Markov Model Application and C++ Library for Rapid and Flexible Development of HMMs (PMID: 24489371)
eldariont/svim (⭐148 · Python) Structural Variant Identification Method using Long Reads (PMID: 30668829)
ncclabsustech/EEGdenoiseNet (⭐148 · Jupyter Notebook) EEGdenoiseNet, a benchmark dataset, that is suited for training and testing deep learning-based EEG denoising models, as well as for comparing the performance across different models. (PMID: 34596046)
theislab/kBET (⭐148 · HTML) An R package to test for batch effects in high-dimensional single-cell RNA sequencing data. (PMID: 30573817)
tsudalab/ChemTS (⭐147 · Python) Molecule Design using Monte Carlo Tree Search with Neural Rollout (PMID: 29435094)
krishnanlab/PecanPy (⭐146 · Python) A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec (PMID: 33760066)
OpenGene/MutScan (⭐145 · C) Detect and visualize target mutations by scanning FastQ files directly (PMID: 29357822)
ZJUDataIntelligence/TEMPO (⭐145 · Python) None (PMID: 36535209)
jotech/gapseq (⭐145 · R) Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks (PMID: 33691770)
mschubert/clustermq (⭐145 · R) R package to send function calls as jobs on LSF, SGE, Slurm, PBS/Torque, or each via SSH (PMID: 31134271)
ncbi/icn3d (⭐145 · JavaScript) web-based protein structure viewer and analysis tool interactively or in batch mode (PMID: 31218344; 35252351)
AdmiralenOla/Scoary (⭐144 · Python) Pan-genome wide association studies (PMID: 27887642)
ekg/seqwish (⭐144 · C++) alignment to variation graph inducer (PMID: 36448683)
healthylaife/MIMIC-IV-Data-Pipeline (⭐144 · Jupyter Notebook) A customizable pipeline for data extraction from MIMIC-IV. (PMID: 36686986)
nadeemlab/DeepLIIF (⭐144 · Python) Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24] (PMID: 37292462; 37841230)
nadeemlab/deepliif (⭐144 · Python) Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24] (PMID: 36118303)
stemangiola/tidyseurat (⭐143 · R) Seurat meets tidyverse. The best of both worlds. (PMID: 34028547)
fenderglass/Ragout (⭐142 · Python) Chromosome-level scaffolding using multiple references (PMID: 24931998)
CBICA/GaNDLF (⭐141 · Python) A generalizable application framework for segmentation, regression, and classification using PyTorch (PMID: 35465060)
getzlab/rnaseqc (⭐141 · C++) Fast, efficient RNA-Seq metrics for quality control and process optimization (PMID: 33677499)
saezlab/decoupler-py (⭐141 · Python) Python package to perform enrichment analysis from omics data. (PMID: 36699385)
CapsuleEndoscope/VirtualCapsuleEndoscopy (⭐140 · C#) VR-Caps: A Virtual Environment for Active Capsule Endoscopy (PMID: 33609920)
CellProfiler/CellProfiler-Analyst (⭐140 · Python) Open-source software for exploring and analyzing large, high-dimensional image-derived data. (PMID: 27354701; 34478488)
LinearFold/LinearFold (⭐140 · C++) The new source code of the LinearFold, linear-time prediction for RNA secondary structures (PMID: 31510672)
deepmodeling/DMFF (⭐140 · Python) DMFF (Differentiable Molecular Force Field) is a Jax-based python package that provides a full differentiable implementation of molecular force field models. (PMID: 37589304)
microsoft/frame-flow (⭐140 · Python) Fast protein backbone generation with SE(3) flow matching. (PMID: 38259348)
sequana/sequana (⭐140 · Jupyter Notebook) Sequana: a set of Snakemake NGS pipelines (PMID: 29361152)
benjjneb/decontam (⭐139 · R) Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data (PMID: 30558668)
OpenBioLink/OpenBioLink (⭐138 · Python) OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data. (PMID: 32339214)
lsyads/fisheye-ORB-SLAM (⭐138 · C++) A real-time robust monocular visual SLAM system based on ORB-SLAM for fisheye cameras, without rectifying or cropping the input images (PMID: 31623266)
mlyg/unified-focal-loss (⭐138 · Python) None (PMID: 34953431)
hewm2008/NGenomeSyn (⭐137 · Perl) Any Way to Show Multi genomic Synteny (PMID: 36883694)
stefpeschel/NetCoMi (⭐137 · R) Network construction, analysis, and comparison for microbial compositional data (PMID: 33264391)
theislab/scCODA (⭐137 · Jupyter Notebook) A Bayesian model for compositional single-cell data analysis (PMID: 34824236)
Teichlab/bbknn (⭐136 · Python) Batch balanced KNN (PMID: 31400197)
gbouras13/pharokka (⭐136 · Python) fast phage annotation program (PMID: 36453861)
marianattestad/assemblytics (⭐136 · JavaScript) Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome. (PMID: 27318204)
masqm/Faster-Mean-Shift (⭐136 · Python) GPU accelerated Faster Mean-shift for cosine embedding clustering (PMID: 33872961)
royfrancis/pophelper (⭐136 · R) An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc. (PMID: 26850166)
SGDDNB/ShinyCell (⭐135 · R) Shiny Interactive Web Apps for Single-Cell Data (PMID: 33774659)
lh3/pangene (⭐135 · C) Constructing a pangenome gene graph (PMID: 38463499)
Ensembl/ensembl-rest (⭐134 · Perl) Language agnostic RESTful data access to Ensembl data over HTTP (PMID: 25236461)
aertslab/cistopic (⭐133 · HTML) cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data (PMID: 30962623)
hakyimlab/MetaXcan (⭐133 · Python) MetaXcan software and manuscript (PMID: 29752479)
imgag/ngs-bits (⭐133 · C++) Short-read sequencing tools (PMID: 27161244; 28130233)
ryanlayer/gqt (⭐133 · C) A genotype query interface. (PMID: 26550772)
walaj/SeqLib (⭐133 · C++) C++ htslib/bwa-mem/fermi interface for interrogating sequence data (PMID: 28011768)
BBillot/SynthSR (⭐132 · Python) A framework for joint super-resolution and image synthesis, without requiring real training data (PMID: 34048902)
gabraham/flashpca (⭐132 · C++) Fast Principal Component Analysis of Large-Scale Genome-Wide Data (PMID: 28475694)
lh3/bedtk (⭐132 · C) A simple toolset for BED files (warning: CLI may change before bedtk becomes stable) (PMID: 32966548)
ATOMconsortium/AMPL (⭐131 · Jupyter Notebook) The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery. (PMID: 32243153)
SheffieldML/GPmat (⭐131 · Matlab) Matlab implementations of Gaussian processes and other machine learning tools. (PMID: 24618470)
hasindu2008/f5c (⭐131 · C) Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration) (PMID: 32758139)
theislab/sc-pert (⭐131 · Jupyter Notebook) Models and datasets for perturbational single-cell omics (PMID: 34139164)
xlucpu/MOVICS (⭐131 · R) Multi-Omics integration and VIsualization in Cancer Subtyping (PMID: 33315104)
Bioconductor/Contributions (⭐130 · None) Contribute Packages to Bioconductor (PMID: 38407991)
brentp/echtvar (⭐130 · Rust) using all the bits for echt rapid variant annotation and filtering (PMID: 36300617)
cruizperez/MicrobeAnnotator (⭐130 · Python) Pipeline for metabolic annotation of microbial genomes (PMID: 33407081)
Merck/BioPhi (⭐128 · Python) BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design. (PMID: 35133949)
galaxyproject/SARS-CoV-2 (⭐128 · Jupyter Notebook) Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures (PMID: 32790776)
lanl001/halc (⭐128 · C++) High Throughput Algorithm for Long Read Error Correction (PMID: 28381259)
Gabaldonlab/redundans (⭐127 · C++) Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes. (PMID: 27131372)
antigenomics/vdjdb-db (⭐127 · Groovy) 🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome! (PMID: 28977646)
churchmanlab/genewalk (⭐127 · Python) GeneWalk identifies relevant gene functions for a biological context using network representation learning (PMID: 33526072)
vals/umis (⭐127 · Python) Tools for processing UMI RNA-tag data (PMID: 28263961)
xulabs/aitom (⭐127 · Python) AI for tomography (PMID: 32722755; 33620460; 34897387)
zhanxw/rvtests (⭐126 · C++) Rare variant test software for next generation sequencing data (PMID: 27153000)
ksahlin/strobealign (⭐125 · C++) Aligns short reads using dynamic seed size with strobemers (PMID: 36522758)
mikessh/vdjtools (⭐125 · Groovy) Post-analysis of immune repertoire sequencing data (PMID: 26606115)
open2c/cooltools (⭐125 · Jupyter Notebook) The tools for your .cool's (PMID: 38709825)
PoisonAlien/trackplot (⭐124 · R) Generate IGV style locus tracks from bigWig files in R (PMID: 38476298)
spetti/SMURF (⭐124 · Python) None (PMID: 36355460)
BlueBrain/NeuroMorphoVis (⭐123 · Python) A lightweight, interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks. (PMID: 29949998)
rrwick/Deepbinner (⭐123 · Python) a signal-level demultiplexer for Oxford Nanopore reads (PMID: 30458005)
bigdatagenomics/mango (⭐122 · Scala) A scalable genome browser. Apache 2 licensed. (PMID: 29308454)
ncbi/TPMCalculator (⭐122 · C++) TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files (PMID: 30379987)
JiekaiLab/scDIOR (⭐121 · HTML) scDIOR: Single cell data IO softwaRe (PMID: 34991457)
echen102/us-pres-elections-2020 (⭐121 · Python) The repository contains a collection of tweets IDs associated with the 2020 U.S. Presidential Elections through 6 months post-inauguration. (PMID: 33824934)
AndersenLab/VCF-kit (⭐120 · Python) VCF-kit: Assorted utilities for the variant call format (PMID: 28093408)
Illumina/canvas (⭐120 · C#) Canvas - Copy number variant (CNV) calling from DNA sequencing data (PMID: 27153601; 29028893)
MRCIEU/PHESANT (⭐120 · R) PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank (PMID: 29040602)
OpenGene/repaq (⭐120 · C) A fast lossless FASTQ compressor with ultra-high compression ratio (PMID: 37811144)
muhammedtalo/COVID-19 (⭐120 · Jupyter Notebook) Automated Detection of COVID-19 Cases Using Deep Neural Networks with X-Ray Images (PMID: 32568675)
parklab/NGSCheckMate (⭐120 · Python) Software program for checking sample matching for NGS data (PMID: 28369524)
songc001/remilo (⭐120 · C++) Reference Assisted Misassembly Detection Algorithm Using Short and Long Reads (PMID: 28961789)
thomas0809/MolScribe (⭐120 · Python) Robust Molecular Structure Recognition with Image-to-Graph Generation (PMID: 36971363)
marbl/parsnp (⭐119 · C++) Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. (PMID: 38724243)
torognes/swarm (⭐119 · C++) A robust and fast clustering method for amplicon-based studies (PMID: 34244702)
baoe/flas (⭐118 · C++) Fast and High Throughput Algorithm for PacBio Long Read Self-Correction (PMID: 30895306)
jdidion/atropos (⭐118 · Python) An NGS read trimming tool that is specific, sensitive, and speedy. (production) (PMID: 28875074)
DiltheyLab/HLA-LA (⭐117 · C++) Fast HLA type inference from whole-genome data (PMID: 30942877)
dzhang32/ggtranscript (⭐117 · R) Visualizing transcript structure and annotation using ggplot2 (PMID: 35751589)
spacegraphcats/spacegraphcats (⭐117 · Standard ML) Indexing & querying large assembly graphs -- in space, no one can hear you miao! (PMID: 32631445)
timolassmann/kalign (⭐117 · C) A fast multiple sequence alignment program. (PMID: 31665271)
yatisht/usher (⭐117 · C++) Ultrafast Sample Placement on Existing Trees (PMID: 34469548; 35731204)
evolbioinfo/gotree (⭐116 · Go) Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language. (PMID: 34396097)
ycwu1997/MC-Net (⭐116 · Python) Official Code for our MedIA paper "Mutual Consistency Learning for Semi-supervised Medical Image Segmentation" (PMID: 35839737)
DeepRank/DeepRank-GNN (⭐115 · Python) Graph Network for protein-protein interface (PMID: 36420989)
biojava/biojava-tutorial (⭐115 · Python) 📖📚An introductory tutorial for BioJava (PMID: 30735498)
carmonalab/UCell (⭐115 · R) Gene set scoring for single-cell data (PMID: 34285779)
OpenGene/GeneFuse (⭐114 · C) Gene fusion detection and visualization (PMID: 29989075)
adamewing/methylartist (⭐114 · Python) Tools for plotting methylation data in various ways (PMID: 35482479)
PheWAS/PheWAS (⭐113 · R) The PheWAS R package (PMID: 29912272)
biocore/mmvec (⭐113 · Python) Neural networks for microbe-metabolite interaction analysis (PMID: 31686038)
guigolab/ggsashimi (⭐113 · Python) Command-line tool for the visualization of splicing events across multiple samples (PMID: 30118475)
hammerlab/cytokit (⭐113 · Jupyter Notebook) Microscopy Image Cytometry Toolkit (PMID: 31477013)
hellloxiaotian/ADNet (⭐113 · Python) Attention-guided CNN for image denoising(Neural Networks,2020) (PMID: 31991307)
oxpig/DeLinker (⭐113 · Python) None (PMID: 32195587)
wanderine/BROCCOLI (⭐113 · C++) BROCCOLI: Software for Fast fMRI Analysis on Many-Core CPUs and GPUs (PMID: 24672471)
ChaissonLab/LRA (⭐112 · C++) Long read aligner (PMID: 34153026)
XiaoleiLiuBio/G2P (⭐112 · None) G2P: A Genome-Wide-Association-Study Simulation Tool for Genotype Simulation, Phenotype Simulation, and Power Evaluation (PMID: 30848784)
althonos/pyhmmer (⭐112 · Cython) Cython bindings and Python interface to HMMER3. (PMID: 37074928)
labsyspharm/ashlar (⭐112 · Python) ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration (PMID: 35972352)
linzhi2013/MitoZ (⭐112 · Shell) MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes (PMID: 30864657)
lykaust15/DeepSimulator (⭐112 · C) The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing. (PMID: 29659695; 31913436)
neuropoly/axondeepseg (⭐112 · Python) Axon/Myelin segmentation using Deep Learning (PMID: 29491478)
thiviyanT/torch-rgcn (⭐112 · Python) A PyTorch implementation of the Relational Graph Convolutional Network (RGCN). (PMID: 36426239)
jameshadfield/phandango (⭐111 · JavaScript) an interactive viewer for populations of bacterial genomes linked by a phylogeny (PMID: 29028899)
mcveanlab/mccortex (⭐111 · C) De novo genome assembly and multisample variant calling (PMID: 29554215)
shubhamchandak94/SPRING (⭐111 · C) FASTQ compression (PMID: 30535063)
juglab/EmbedSeg (⭐110 · Python) Code Implementation for EmbedSeg, an Instance Segmentation Method for Microscopy Images (PMID: 35926335)
oxpig/AbLang (⭐110 · Python) AbLang: A language model for antibodies (PMID: 36699403)
rrwick/perfect-bacterial-genome-tutorial (⭐110 · Python) None (PMID: 36862631)
OpenGene/fastv (⭐109 · C++) An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19. (PMID: 33003197)
OpenGene/gencore (⭐109 · C++) Generate duplex/single consensus reads to reduce sequencing noises and remove duplications (PMID: 31881822)
igvteam/igv-webapp (⭐109 · JavaScript) IGV Web App (PMID: 36562559)
lingluodlut/Att-ChemdNER (⭐109 · Python) Att-ChemdNER (PMID: 29186323)
mikevoets/jama16-retina-replication (⭐109 · Python) JAMA 2016; 316(22) Replication Study (PMID: 31170223)
molgenis/molgenis (⭐109 · Java) MOLGENIS - for scientific data: management, exploration, integration and analysis. (PMID: 27153686; 29036577; 29599418)
BioinfoMachineLearning/Bio-Diffusion (⭐108 · Python) A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization (PMID: 36798459)
RabadanLab/arcasHLA (⭐108 · Python) Fast and accurate in silico inference of HLA genotypes from RNA-seq (PMID: 31173059)
YaqiangCao/cLoops (⭐108 · Python) Accurate and flexible loops calling tool for 3D genomic data. (PMID: 31504161)
broadinstitute/ml4h (⭐108 · Jupyter Notebook) None (PMID: 35157695)
cozygene/FEAST (⭐108 · R) Fast expectation maximization for microbial source tracking (PMID: 31182859)
lh3/fermikit (⭐108 · TeX) De novo assembly based variant calling pipeline for Illumina short reads (PMID: 26220959)
ChristofferFlensburg/SuperFreq (⭐107 · R) Analysis pipeline for cancer sequencing data (PMID: 34132781)
OpenTreeOfLife/opentree (⭐107 · JavaScript) Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo. (PMID: 25940563)
RagnarGrootKoerkamp/astar-pairwise-aligner (⭐107 · Rust) A pairwise sequence aligner written in Rust (PMID: 38265119)
Xinglab/DARTS (⭐107 · Python) Deep-learning Augmented RNA-seq analysis of Transcript Splicing (PMID: 30923373)
bioinfomaticsCSU/deepsignal (⭐107 · Python) Detecting methylation using signal-level features from Nanopore sequencing reads (PMID: 30994904)
cansyl/DEEPscreen (⭐107 · Python) DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images (PMID: 33209251)
ncbi/MedCPT (⭐107 · Python) Code for MedCPT, a model for zero-shot biomedical information retrieval. (PMID: 37930897)
parklab/bamsnap (⭐107 · HTML) None (PMID: 33416869)
szpiech/selscan (⭐107 · C) Haplotype based scans for selection (PMID: 25015648; 38180866)
whitead/molbloom (⭐107 · Python) Molecular bloom filter tool (PMID: 37828615)
FePhyFoFum/phyx (⭐106 · C++) phylogenetics tools for linux (and other mostly posix compliant) computers (PMID: 28174903)
biopragmatics/bioregistry (⭐106 · Python) 📮 An integrative registry of biological databases, ontologies, and nomenclatures. (PMID: 36402838)
chrishah/MITObim (⭐106 · Perl) MITObim - mitochondrial baiting and iterative mapping (PMID: 23661685)
lh3/minimap (⭐106 · C) This repo is DEPRECATED. Please use minimap2, the successor of minimap. (PMID: 27153593)
morrislab/phylowgs (⭐106 · Python) Application for inferring subclonal composition and evolution from whole-genome sequencing data. (PMID: 25786235)
rezacsedu/XAI-for-bioinformatics (⭐106 · Jupyter Notebook) Explainable AI for Bioinformatics (PMID: 37478371)
vanessajurtz/lasagne4bio (⭐106 · Jupyter Notebook) None (PMID: 28961695)
xiaochuanle/MECAT (⭐106 · C++) MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads (PMID: 28945707)
yangao07/abPOA (⭐106 · C) abPOA: an SIMD-based C library for fast partial order alignment using adaptive band (PMID: 33165528)
SunPengChuan/wgdi (⭐105 · Python) WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes (PMID: 36307977)
csyben/PYRO-NN (⭐105 · Python) Python Reconstruction Operators in Neural Networks. High level python API for PYRO-NN-Layers (PMID: 31389023)
ncbi/SKESA (⭐105 · C++) SKESA assembler (PMID: 30286803)
zhjohnchan/M3AE (⭐105 · Python) [MICCAI-2022] This is the official implementation of Multi-Modal Masked Autoencoders for Medical Vision-and-Language Pre-Training. (PMID: 37976867)
MASILab/SLANTbrainSeg (⭐104 · Python) Deep Whole Brain Segmentation Using SLANT Method (PMID: 30910724; 34999162)
gaocong13/Projective-Spatial-Transformers (⭐104 · Python) Generalizing Spatial Transformers to Projective Geometry with Applications to 2D/3D Registration (PMID: 33135014)
hahnlab/CAFE5 (⭐104 · C++) Version 5 of the CAFE phylogenetics software (PMID: 33325502)
bvieth/powsimR (⭐103 · HTML) Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses. (PMID: 29036287)
louiejtaylor/grabseqs (⭐103 · Python) A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA (PMID: 32154830)
mabessa/F3DAS (⭐103 · Python) Framework for Data-Driven Design & Analysis of Structures & Materials (F3DASM) (PMID: 31608516)
openPupil/Open-PupilEXT (⭐103 · C++) Official implementation of a free pupillometry platform called PupilEXT proposed in the article "PupilEXT: flexible open-source platform for high resolution pupillometry in vision research". (PMID: 34220432)
BaderLab/saber (⭐102 · Python) Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable. (PMID: 31218364)
CDDLeiden/DrugEx (⭐102 · Jupyter Notebook) De Novo Drug Design with RNNs and Transformers (PMID: 37272707)
SBRG/ssbio (⭐102 · Python) A Python framework for structural systems biology (PMID: 29444205)
hakyimlab/PrediXcan (⭐102 · Python) PrediXcan Project (PMID: 27835642)
ratschlab/spladder (⭐102 · Python) Tool for the detection and quantification of alternative splicing events from RNA-Seq data. (PMID: 26873928)
rnabioco/clustifyr (⭐102 · R) Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets (PMID: 32765839)
vaquerizaslab/fanc (⭐102 · Python) FAN-C: Framework for the ANalysis of C-like data (PMID: 33334380)
yanwu2014/swne (⭐102 · R) Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets (PMID: 30528274)
BigDataBiology/SemiBin (⭐101 · Python) SemiBin: metagenomics binning with self-supervised deep learning (PMID: 37387171)
CostaLab/reg-gen (⭐101 · Python) Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data. (PMID: 36879236)
grimmlab/MicrobiomeBestPracticeReview (⭐101 · Shell) Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing (PMID: 31848574)
zhxiaokang/RASflow (⭐101 · HTML) RNA-Seq analysis workflow (PMID: 32183729)
ZJUFanLab/bulk2space (⭐100 · Jupyter Notebook) a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles (PMID: 36310179)
arseha/peakonly (⭐100 · Python) None (PMID: 31841624)
hugheslab/snpgenie (⭐100 · Perl) Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data (PMID: 26227143)
mgalardini/pyseer (⭐100 · Python) SEER, reimplemented in python 🐍🔮 (PMID: 30535304)
MathOnco/NeoPredPipe (⭐99 · Python) Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan. (PMID: 31117948)
MolecularAI/DockStream (⭐99 · Python) DockStream: A Docking Wrapper to Enhance De Novo Molecular Design (PMID: 34789335)
brentp/duphold (⭐99 · Nim) don't get DUP'ed or DEL'ed by your putative SVs. (PMID: 31222198)
evoldoers/biomake (⭐99 · Prolog) GNU-Make-like utility for managing builds and complex workflows (PMID: 28486579)
j3xugit/RaptorX-3DModeling (⭐99 · C) Note that current version does not include search of very large metagenome data. For some proteins, metagenome data is important. We will update this as soon as possible. (PMID: 33961022)
zeeev/wham (⭐99 · C++) Structural variant detection and association testing (PMID: 26625158)
3DGenomes/tadbit (⭐98 · Python) TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models (PMID: 28723903)
MannLabs/alphapeptdeep (⭐98 · Jupyter Notebook) Deep learning framework for proteomics (PMID: 36433986)
abhi4ssj/few-shot-segmentation (⭐98 · Python) PyTorch implementation of 'Squeeze and Excite' Guided Few Shot Segmentation of Volumetric Scans (PMID: 31630012)
jlianglab/Fixed-Point-GAN (⭐98 · Python) Official implementation of Fixed-Point GAN - ICCV 2019 (PMID: 32612486)
mossmatters/HybPiper (⭐98 · Python) Recovering genes from targeted sequence capture data (PMID: 27437175)
JLiangLab/DiRA (⭐97 · Python) Official PyTorch Implementation for DiRA: Discriminative, Restorative, and Adversarial Learning for Self-supervised Medical Image Analysis - CVPR 2022 (PMID: 36313959; 38537414)
SysBioChalmers/RAVEN (⭐97 · MATLAB) The RAVEN Toolbox for genome scale model reconstruction, curation and analysis. (PMID: 30335785)
labsquare/cutevariant (⭐97 · Python) A standalone and free application to explore genetics variations from VCF file (PMID: 36699349)
makism/dyconnmap (⭐97 · Python) A dynamic connectome mapping module in python. (PMID: 34250674)
GATB/bcalm (⭐96 · Python) compacted de Bruijn graph construction in low memory (PMID: 27307618)
citiususc/veryfasttree (⭐96 · C++) Efficient phylogenetic tree inference for massive taxonomic datasets (PMID: 32573652)
lh3/bgt (⭐96 · C) Flexible genotype query among 30,000+ samples whole-genome (PMID: 26500154)
oxpig/ImmuneBuilder (⭐96 · Jupyter Notebook) Predict the structure of immune receptor proteins (PMID: 37248282)
verilylifesciences/genomewarp (⭐96 · Java) GenomeWarp translates genetic variants from one genome assembly version to another. (PMID: 30916319)
AlexandrovLab/SigProfilerMatrixGenerator (⭐95 · Python) SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools. (PMID: 31470794; 37605126)
BEETL/BEETL (⭐94 · C++) BEETL (PMID: 22556365; 24950811)
ZJUFanLab/scDeepSort (⭐94 · Python) Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network (PMID: 34500471)
aistairc/DeepEventMine (⭐94 · Python) DeepEventMine: End-to-end Neural Nested Event Extraction from Biomedical Texts (PMID: 33141147)
genomicsITER/NanoCLUST (⭐94 · Nextflow) NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads (PMID: 33079990)
immunogenomics/symphony (⭐94 · Jupyter Notebook) Efficient and precise single-cell reference atlas mapping with Symphony (PMID: 34620862)
microsoft/genomicsnotebook (⭐94 · Jupyter Notebook) Jupyter Notebooks on Azure for Genomics Data Analysis (PMID: 36726729)
nmquijada/tormes (⭐94 · Shell) Making whole bacterial genome sequencing data analysis easy (PMID: 30957837)
pulimeng/DeepDrug3D (⭐94 · Python) A convolutional neural network for classifying binding pockets based on spatial and chemical information extracted from the pockets. (PMID: 30716081)
roblanf/sangeranalyseR (⭐94 · R) functions to analyse sanger sequencing reads in R (PMID: 33591316)
bbci/wyrm (⭐93 · Python) Python toolbox for Brain-Computer Interfacing (BCI) (PMID: 26001643)
futianfan/clinical-trial-outcome-prediction (⭐93 · Python) benchmark dataset and Deep learning method (Hierarchical Interaction Network, HINT) for clinical trial approval probability prediction, published in Cell Patterns 2022. (PMID: 35465223)
jbohnslav/deepethogram (⭐93 · Python) None (PMID: 34473051)
ropensci/nasapower (⭐93 · R) API Client for NASA POWER Global Meteorology, Surface Solar Energy and Climatology in R (PMID: 34039412)
theosanderson/taxonium (⭐93 · JavaScript) A tool for exploring very large trees in the browser (PMID: 36377483; 36453872)
treangen/MetAMOS (⭐93 · Roff) A metagenomic and isolate assembly and analysis pipeline built with AMOS (PMID: 23320958)
cytoscape/cyjShiny (⭐92 · JavaScript) An R/shiny widget for cytoscape.js (PMID: 37585474)
twolinin/LongPhase (⭐92 · C) None (PMID: 35104333)
zstephens/neat-genreads (⭐92 · Python) NEAT read simulation tools (PMID: 27893777)
Illumina/Pisces (⭐91 · C#) Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows. (PMID: 30304370)
bcgsc/ntHash (⭐91 · C++) Fast hash function for DNA/RNA sequences (PMID: 36000872)
biocore/deblur (⭐91 · Python) Deblur is a greedy deconvolution algorithm based on known read error profiles. (PMID: 28289731)
caitiecollins/treeWAS (⭐91 · R) treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes (PMID: 29401456)
qubekit/QUBEKit (⭐91 · Python) Quantum Mechanical Bespoke Force Field Derivation Toolkit (PMID: 35792069)
vanderschaarlab/AutoPrognosis (⭐91 · Python) A system for automating the design of predictive modeling pipelines tailored for clinical prognosis. (PMID: 37347752)
yuhoo0302/Segment-Anything-Model-for-Medical-Images (⭐91 · Python) Codes and models for Medical Image Analysis (MIA) 2023 paper. Segment Anything Model for Medical Images?. (PMID: 38086235)
bcgsc/ARCS (⭐90 · C++) 🌈Scaffold genome sequence assemblies using linked or long read sequencing data (PMID: 29069293)
freeseek/score (⭐90 · C) Tools to work with GWAS-VCF summary statistics files (PMID: 38261650)
modeloriented/survex (⭐90 · R) Explainable Machine Learning in Survival Analysis (PMID: 38039146)
nawrockie/vadr (⭐90 · Perl) Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation (PMID: 32448124)
parashardhapola/scarf (⭐90 · Python) Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop. (PMID: 35941103)
BioJulia/BioStructures (⭐89 · Julia) A Julia package to read, write and manipulate macromolecular structures (PMID: 32407511)
FastTrackOrg/FastTrack (⭐89 · C++) FastTrack is a cross-platform application designed to track multiple objects in video recording. (PMID: 33571205)
bergmanlab/mcclintock (⭐89 · Python) Meta-pipeline to identify transposable element insertions using next generation sequencing data (PMID: 28637810; 37452430)
ccipd/MRQy (⭐89 · JavaScript) MRQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) data. (PMID: 33176026)
cpockrandt/genmap (⭐89 · C++) GenMap - Fast and Exact Computation of Genome Mappability (PMID: 32246826)
giesselmann/nanopype (⭐89 · Python) Snakemake pipelines for nanopore sequencing data archiving and processing (PMID: 31192347)
jodyphelan/TBProfiler (⭐89 · Python) Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data (PMID: 33317631)
mozack/abra2 (⭐89 · Java) ABRA2 (PMID: 30649250)
mr7495/COVID-CTset (⭐89 · Python) Large Covid-19 CT scans dataset from the paper: https://doi.org/10.1016/j.bspc.2021.102588 (PMID: 33821166)
ShuweiShao/AF-SfMLearner (⭐88 · Python) [MedIA2022 & ICRA2021] Self-Supervised Monocular Depth and Ego-Motion Estimation in Endoscopy: Appearance Flow to the Rescue (PMID: 35016079)
bigchem/transformer-cnn (⭐88 · Python) Transformer CNN for QSAR/QSPR modelling (PMID: 33431004)
fwhelan/coinfinder (⭐88 · C++) A tool for the identification of coincident (associating and dissociating) genes in pangenomes. (PMID: 32100706)
gamcil/cblaster (⭐88 · HTML) Find clustered hits from a BLAST search (PMID: 36700093)
mrzResearchArena/PyFeat (⭐88 · Python) A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences (PMID: 30850831)
romanhaa/Cerebro (⭐88 · HTML) Visualization of scRNA-seq data. (PMID: 31764967)
BUStools/bustools (⭐87 · C) Tools for working with BUS files (PMID: 37129540)
ChristopherWilks/megadepth (⭐87 · C++) BigWig and BAM utilities (PMID: 33693500)
CogStack/SemEHR (⭐87 · JavaScript) Surfacing Semantic Data from Clinical Notes in Electronic Health Records for Tailored Care, Trial Recruitment and Clinical Research (PMID: 29361077)
KatherLab/HIA (⭐87 · Python) Histopathology Image Analysis (PMID: 35588568)
jminnier/STARTapp (⭐87 · HTML) The START App: R Shiny Transcriptome Analysis Resource Tool (PMID: 28171615)
orbkit/orbkit (⭐87 · Python) A Toolbox for Post-Processing Quantum Chemical Wavefunction Data (PMID: 27043934)
wdecoster/methplotlib (⭐87 · Python) Plotting tools for nanopore methylation data (PMID: 32053166)
CenterForMedicalGeneticsGhent/WisecondorX (⭐86 · Python) WisecondorX — An evolved WISECONDOR (PMID: 30566647)
Superzchen/iLearnPlus (⭐86 · Python) iLearnPlus is the first machine-learning platform with both graphical- and web-based user interface that enables the construction of automated machine-learning pipelines for computational analysis and predictions using nucleic acid and protein sequences. (PMID: 33660783)
blab/nextflu (⭐86 · JavaScript) Real-time tracking of influenza evolution (PMID: 26115986)
budach/pysster (⭐86 · Python) pysster: Learning Sequence And Structure Motifs In Biological Sequences Using Convolutional Neural Networks (PMID: 29659719)
cafferychen777/ggpicrust2 (⭐86 · R) Make Picrust2 Output Analysis and Visualization Easier (PMID: 37527009)
changwn/scFEA (⭐86 · Jupyter Notebook) single cell Flux Estimation Analysis (scFEA) Try the below web server! (PMID: 37216602)
chuiqin/irGSEA (⭐86 · R) The integration of single cell rank-based gene set enrichment analysis (PMID: 38801700)
htseq/htseq (⭐86 · Python) HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. (PMID: 35561197)
meren/illumina-utils (⭐86 · Python) A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline). (PMID: 23799126)
parklab/xTea (⭐86 · Python) Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics (PMID: 34158502)
EtienneCmb/tensorpac (⭐85 · Python) Phase-Amplitude Coupling under Python (PMID: 33119593)
gui11aume/starcode (⭐85 · C) All pairs search and sequence clustering (PMID: 25638815)
llnl/fast (⭐85 · Python) Fusion models for Atomic and molecular STructures (FAST) (PMID: 33754707)
ramiromagno/gwasrapidd (⭐85 · R) gwasrapidd: an R package to query, download and wrangle GWAS Catalog data (PMID: 31373609)
uwrit/leaf (⭐85 · TypeScript) Leaf Clinical Data Explorer (PMID: 31592524)
0liliulei/Mem3D (⭐84 · Python) None (PMID: 36327652)
carmonalab/scGate (⭐84 · R) marker-based purification of cell types from single-cell RNA-seq datasets (PMID: 35258562)
cdcgov/microbetrace (⭐84 · TypeScript) The Visualization Multitool for Molecular Epidemiology and Bioinformatics (PMID: 34492010)
lanagarmire/DeepImpute (⭐84 · Python) An accurate and efficient deep learning method for single-cell RNA-seq data imputation (PMID: 31627739)
openbiox/UCSCXenaShiny (⭐84 · R) 📊 An R package for interactively exploring UCSC Xena https://xenabrowser.net/datapages/; Book: https://lishensuo.github.io/UCSCXenaShiny_Book; App online: https://shiny.hiplot.cn/ucsc-xena-shiny/, https://shiny.zhoulab.ac.cn/UCSCXenaShiny (PMID: 34323947)
smirarab/pasta (⭐84 · Python) PASTA (Practical Alignment using SATe and Transitivity) (PMID: 29931282)
vanallenlab/comut (⭐84 · Python) CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots (PMID: 32502231)
eldariont/svim-asm (⭐83 · Python) Structural Variant Identification Method using Genome Assemblies (PMID: 33346817)
yjx1217/simuG (⭐83 · Perl) simuG: a general-purpose genome simulator (PMID: 31116378)
balbasty/nitorch (⭐82 · Python) Neuroimaging in PyTorch (PMID: 34271531)
bcgsc/RNA-Bloom (⭐82 · Java) 🌺 reference-free transcriptome assembly for short and long reads (PMID: 37217540)
catavallejos/BASiCS (⭐82 · R) BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version (PMID: 27083558)
ncbi/fcs (⭐82 · None) Foreign Contamination Screening caller scripts and documentation (PMID: 38409096)
nunofonseca/irap (⭐82 · R) integrated RNA-seq Analysis Pipeline (PMID: 28369191)
shervinmin/DeepCovid (⭐82 · Python) None (PMID: 32781377)
splatlab/squeakr (⭐82 · C++) Squeakr: An Exact and Approximate k -mer Counting System (PMID: 29444235)
MICCoM/SSAGES-public (⭐81 · C++) Software Suite for Advanced General Ensemble Simulations (PMID: 29390830)
PayneLab/cptac (⭐81 · Jupyter Notebook) Python packaging for CPTAC data (PMID: 33560848)
Vini2/GraphBin (⭐81 · Python) ✨🧬 Refined binning of metagenomic contigs using assembly graphs (PMID: 32167528)
nstrodt/UDSMProt (⭐81 · Python) Protein sequence classification with self-supervised pretraining (PMID: 31913448)
xie186/ViewBS (⭐81 · Perl) ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data (PMID: 29087450)
CoSMoMVPA/CoSMoMVPA (⭐80 · MATLAB) A lightweight multivariate pattern analysis (MVPA) toolbox in Matlab / Octave (PMID: 27499741)
arthurpessa/ordpy (⭐80 · Python) A Python package for data analysis with permutation entropy and ordinal network methods. (PMID: 34241315)
bcgsc/ntjoin (⭐80 · Python) 🔗Genome assembly scaffolder using minimizer graphs (PMID: 32311025)
crazyhottommy/scclusteval (⭐80 · R) Single Cell Cluster Evaluation (PMID: 33165513)
gevaertlab/MultimodalPrognosis (⭐80 · Python) Deep Learning with Multimodal Representation for Pancancer Prognosis Prediction (PMID: 31510656)
jermp/sshash (⭐80 · C++) A compressed, associative, exact, and weighted dictionary for k-mers. (PMID: 35758794)
smirarab/sepp (⭐80 · Python) Ensemble of HMM methods (SEPP, TIPP, UPP) (PMID: 26076734; 28185571; 33471121; 34791036)
splatlab/mantis (⭐80 · C++) Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index (PMID: 35325039)
zzstefan/BrainNetClass (⭐80 · MATLAB) None (PMID: 32163221)
DlutMedimgGroup/AnatomySketch-Software (⭐79 · C++) A medical image segmentation software supporting user interventions and user-defined funtion extention (PMID: 35768752)
MeHelmy/princess (⭐79 · Python) None (PMID: 34521442)
RemiAllio/MitoFinder (⭐79 · Python) MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data (PMID: 32243090)
frankvogt/vcf2gwas (⭐79 · Python) Python API for comprehensive GWAS analysis using GEMMA (PMID: 34636840)
glennhickey/progressiveCactus (⭐79 · Python) Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules (PMID: 25138168)
moiexpositoalonsolab/grenepipe (⭐79 · Python) A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads. (PMID: 36053180)
scvae/scvae (⭐79 · Python) Deep learning for single-cell transcript counts (PMID: 32415966)
xavierdidelot/BactDating (⭐79 · R) Bayesian inference of ancestral dates on bacterial phylogenetic trees (PMID: 30184106)
JLiangLab/SemanticGenesis (⭐78 · Python) Official Keras & PyTorch Implementation and Pre-trained Models for Semantic Genesis - MICCAI 2020 (PMID: 35695848)
KeenThera/SECSE (⭐78 · Python) Systemic Evolutionary Chemical Space Exploration for Drug Discovery (PMID: 35365231)
Vaa3D/vaa3d (⭐78 · None) www.vaa3d.org (PMID: 37213868)
genome/gms (⭐78 · Perl) The Genome Modeling System installer (PMID: 26158448)
mdsufz/MuDoGeR (⭐78 · Shell) MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy. (PMID: 37994269)
sjspielman/pyvolve (⭐78 · Python) Python library to simulate evolutionary sequence data (PMID: 26397960)
stephens999/ashr (⭐78 · R) An R package for adaptive shrinkage (PMID: 27756721)
MannLabs/alphatims (⭐77 · Python) An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistry. (PMID: 34543758)
Oshlack/JAFFA (⭐77 · C++) JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions (PMID: 26019724; 34991664)
arzwa/wgd (⭐77 · Python) Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd. (PMID: 30398564)
calico/solo (⭐77 · Python) software to detect doublets (PMID: 32592658)
chaoszhang/ASTER (⭐77 · C++) Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL) (PMID: 36094339)
jokergoo/rGREAT (⭐77 · R) GREAT Analysis - Functional Enrichment on Genomic Regions (PMID: 36394265)
seqan/flexbar (⭐77 · C++) flexible barcode and adapter removal (PMID: 28541403)
tderrien/FEELnc (⭐77 · Perl) FEELnc : FlExible Extraction of LncRNA (PMID: 28053114)
TinkerTools/tinker-hp (⭐76 · C) Tinker-HP: High-Performance Massively Parallel Evolution of Tinker on CPUs & GPUs (PMID: 33173801; 33755446)
asad/ReactionDecoder (⭐76 · Java) Reaction Decoder Tool (RDT) - Atom Atom Mapping Tool (PMID: 27153692)
bcgsc/ntCard (⭐76 · C++) Estimating k-mer coverage histogram of genomics data (PMID: 28453674)
fkong7/MeshDeformNet (⭐76 · Python) A deep-learning approach for direct whole-heart mesh reconstruction (PMID: 34543913)
s312569/clj-biosequence (⭐76 · Clojure) A Clojure library designed to make the manipulation of biological sequence data easier. (PMID: 24794932)
HRGV/phyloFlash (⭐75 · Perl) phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset. (PMID: 33109753)
VoiceBeer/MS-MDA (⭐75 · Jupyter Notebook) Code of paper MS-MDA: Multisource Marginal Distribution Adaptation for Cross-subject and Cross-session EEG Emotion Recognition (PMID: 34949983)
canlab/MediationToolbox (⭐75 · HTML) Single-level and multi-level mediation analyses for any kind of data, with bootstrap-based significance testing. Neuroimaging-oriented functions allow for mediation effect parametric mapping (mapping of mediation effects across the brain) and multivariate mediation. (PMID: 36569614)
BioEasy/EasyCodeML (⭐74 · C) EasyCodeML: A visual tool for analysis of selection using CodeML (PMID: 31015974)
PapenfussLab/bionix (⭐74 · Nix) Functional highly reproducible bioinformatics pipelines (PMID: 33205815)
bigbio/proteomics-metadata-standard (⭐74 · Python) The Proteomics Experimental Design file format: Standard for experimental design annotation (PMID: 32786688)
compgenome365/TCGA-Assembler-2 (⭐74 · R) TCGA-Assembler 2 (PMID: 29272348)
jwalabroad/VariantBam (⭐74 · Makefile) Filtering and profiling of next-generational sequencing data using region-specific rules (PMID: 27153727)
lh3/fermi (⭐74 · C) A WGS de novo assembler based on the FMD-index for large genomes (PMID: 22569178)
netZoo/netZooPy (⭐74 · Jupyter Notebook) netZooPy is a network biology package implemented in Python. (PMID: 35156023)
seqan/lambda (⭐74 · C++) LAMBDA – the Local Aligner for Massive Biological DatA (PMID: 38485699)
DerKevinRiehl/TransposonUltimate (⭐73 · None) TransposonUltimate - a holistic set of tools for transposon identification (PMID: 35234904)
cosconatilab/PyRMD (⭐73 · Python) AI-powered Virtual Screening (PMID: 34270903; 37552222)
grailbio/bio (⭐73 · Go) Bioinformatic infrastructure libraries (PMID: 31510681)
rsinghlab/pyaging (⭐73 · Jupyter Notebook) A Python-based compendium of GPU-optimized aging clocks. (PMID: 38603598)
xiezhq/ISEScan (⭐73 · Python) A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome (PMID: 29077810)
FangpingWan/NeoDTI (⭐72 · Python) NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions (PMID: 30561548)
LiLabAtVT/DeepTE (⭐72 · Python) Neural network classification of TE (PMID: 32415954)
MannLabs/alphamap (⭐72 · Jupyter Notebook) An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge. (PMID: 34586352)
Phlya/coolpuppy (⭐72 · Python) A versatile tool to perform pile-up analysis on Hi-C data in .cool format. (PMID: 32003791)
SaskiaFreytag/schex (⭐72 · R) None (PMID: 31794001)
ddarriba/modeltest (⭐72 · C++) Best-fit model selection (PMID: 31432070)
diazlab/CONICS (⭐72 · R) CONICS: COpy-Number analysis In single-Cell RNA-Sequencing (PMID: 29897414)
illumina/REViewer (⭐72 · C++) A tool for visualizing alignments of reads in regions containing tandem repeats (PMID: 35948990)
instadeepai/manyfold (⭐72 · Python) 🧬 ManyFold: An efficient and flexible library for training and validating protein folding models (PMID: 36495196)
montilab/hypeR (⭐72 · R) An R Package for Geneset Enrichment Workflows (PMID: 31498385)
natir/yacrd (⭐72 · Rust) Yet Another Chimeric Read Detector (PMID: 32315402)
ncbi/SSDraw (⭐72 · Jupyter Notebook) None (PMID: 37953705)
Liuxg16/GeoPPI (⭐71 · Python) None (PMID: 34347784)
ShellyCoder/cellcall (⭐71 · R) inferring cell-cell communication from scRNA-seq of ligand-receptor (PMID: 34331449)
gnina/models (⭐71 · Python) Trained caffe models (PMID: 32865404)
lh3/dna-nn (⭐71 · C) Model and predict short DNA sequence features with neural networks (PMID: 30989183)
mateidavid/nanocall (⭐71 · C++) An Oxford Nanopore Basecaller (PMID: 27614348)
pymodproject/pymod (⭐71 · Python) PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL. (PMID: 28158668; 33010156)
samsledje/D-SCRIPT (⭐71 · Jupyter Notebook) A structure-aware interpretable deep learning model for sequence-based prediction of protein-protein interactions (PMID: 37897686)
scwatts/FastSpar (⭐71 · C++) Rapid and scalable correlation estimation for compositional data (PMID: 30169561)
GfellerLab/EPIC (⭐70 · R) Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data. (PMID: 32124324)
MaterialsDiscovery/PyChemia (⭐70 · Python) Python Materials Discovery Framework (PMID: 27232694)
chainsawriot/rang (⭐70 · R) 🐶 (Re)constructing R computational environments (PMID: 37289797)
chentao1999/MedicalRelationExtraction (⭐70 · Python) The depository support training and testing BERT-CNN model on three medical relation extraction corpora: BioCreative V CDR task corpus, traditional Chinese medicine literature corpus, and i2b2 temporal relation corpus. (PMID: 31800044)
comprna/METEORE (⭐70 · R) Automatic DNA methylation detection from nanopore tools and their consensus model (PMID: 34103501)
dereneaton/ipyrad (⭐70 · Jupyter Notebook) Interactive assembly and analysis of RAD-seq data sets (PMID: 31904816)
histocartography/hact-net (⭐70 · Python) None (PMID: 34781160)
jltsiren/gcsa2 (⭐70 · C++) BWT-based index for graphs (PMID: 31406990)
lanagarmire/DeepProg (⭐70 · Python) Deep-Learning framework for multi-omic and survival data integration (PMID: 34261540)
lmmpf/PyAutoFEP (⭐70 · Python) PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods (PMID: 34142828)
marekborowiec/AMAS (⭐70 · Python) Calculate summary statistics and manipulate multiple sequence alignments (PMID: 26835189)
microsoft/IGT-Intermolecular-Graph-Transformer (⭐70 · None) None (PMID: 35514186)
mozack/abra (⭐70 · Java) Assembly Based ReAligner (PMID: 24907369)
RitchieLab/eQTpLot (⭐69 · R) Visualization of Colocalization Between eQTL and GWAS Data (PMID: 34273980)
carmonalab/STACAS (⭐69 · R) R package for semi-supervised single-cell data integration (PMID: 32845323)
citiususc/SparkBWA (⭐69 · C) SparkBWA is a new tool that exploits the capabilities of a Big Data technology as Apache Spark to boost the performance of one of the most widely adopted sequence aligner, the Burrows-Wheeler Aligner (BWA). (PMID: 27182962)
meringlab/FlashWeave (⭐69 · Julia) Inference of microbial interaction networks from large-scale heterogeneous abundance data (PMID: 31542415)
vertgenlab/gonomics (⭐69 · Go) A collection of genomics software tools written in Go (golang). (PMID: 37624924)
yukiteruono/pbsim2 (⭐69 · C++) PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores (PMID: 32976553)
zuoxinian/CCS (⭐69 · MATLAB) Connectome Computation System (PMID: 36738058)
GanjinZero/CODER (⭐68 · Python) CODER: Knowledge infused cross-lingual medical term embedding for term normalization. [JBI, ACL-BioNLP 2022] (PMID: 34990838)
Genentech/pviz (⭐68 · JavaScript) Pviz (PMID: 25147360)
TheWebMonks/meshmonk (⭐68 · C++) Open mesh-to-mesh registration framework (PMID: 32746977)
eturro/mmseq (⭐68 · C++) Haplotype, isoform and gene level expression analysis using multi-mapping RNA-seq reads (PMID: 24281695)
lh3/bfc (⭐68 · TeX) High-performance error correction for Illumina resequencing data (PMID: 25953801)
lh3/ropebwt2 (⭐68 · TeX) Incremental construction of FM-index for DNA sequences (PMID: 25107872)
sebwouters/chemps2 (⭐68 · C++) CheMPS2: a spin-adapted implementation of DMRG for ab initio quantum chemistry (PMID: 27497552)
tlemane/kmtricks (⭐68 · C++) modular k-mer count matrix and Bloom filter construction for large read collections (PMID: 36699393)
Pbdas/epa-ng (⭐67 · C++) Massively parallel phylogenetic placement of genetic sequences (PMID: 30165689)
broadinstitute/oncotator (⭐67 · Python) None (PMID: 25703262)
dphansti/Sushi (⭐67 · R) Tools for visualizing genomics data (PMID: 24903420)
epiviz/epiviz (⭐67 · JavaScript) EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features. (PMID: 31782758)
hdaoud/ORBSLAMM (⭐67 · C++) None (PMID: 29702697)
simonvh/fluff (⭐67 · Python) Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments. (PMID: 27547532)
zoecastillo/microbiomeExplorer (⭐67 · R) The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson. (PMID: 32960962)
AllonKleinLab/SPRING (⭐66 · OpenEdge ABL) None (PMID: 29228172)
Graylab/GeoDock (⭐66 · Python) Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer. (PMID: 38148272)
brinkmanlab/GenomeD3Plot (⭐66 · JavaScript) SVG based genome viewer written in javascript using D3 (PMID: 26093150)
czodrowskilab/Machine-learning-meets-pKa (⭐66 · Jupyter Notebook) None (PMID: 32226607)
fanglab/nanodisco (⭐66 · R) nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing. (PMID: 33820988)
huangzhii/SALMON (⭐66 · Python) SALMON: Survival Analysis Learning with Multi-Omics Neural Networks (PMID: 30906311)
kweimann/ecg-transfer-learning (⭐66 · Python) None (PMID: 33664343)
neurogenomics/rworkflows (⭐66 · HTML) Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳. (PMID: 38167858)
niemasd/TreeCluster (⭐66 · Python) Efficient phylogenetic clustering of viral sequences (PMID: 31437182)
robotoD/GenoVi (⭐66 · Python) GenoVi, an automated customizable circular genome visualizer for bacteria and archaea (PMID: 37014908)
aatapa/RLScore (⭐65 · Python) None (PMID: 30329015)
amcrisan/Adjutant (⭐65 · R) Runs a pubmed query, returns results and allows user to explore high-level structure of returned documents (PMID: 30875428)
bede/hostile (⭐65 · Python) Precise host read removal (PMID: 38039142)
deprekate/PHANOTATE (⭐65 · Python) PHANOTATE: a tool to annotate phage genomes. (PMID: 31329826)
jwintersinger/kablammo (⭐65 · JavaScript) Interactive, web-based BLAST results visualization tool. Accessible at https://kablammo.wasmuthlab.org. (PMID: 25481007)
lidaof/eg-react (⭐65 · JavaScript) WashU Epigenome Browser (PMID: 32941613)
powellgenomicslab/scPred (⭐65 · R) scPred package for cell type prediction from scRNA-seq data (PMID: 31829268)
simonhmartin/twisst (⭐65 · Python) Topology weighting by iterative sampling of sub-trees (PMID: 28341652)
superlouis/GATGNN (⭐65 · Python) Pytorch Repository for our work: Graph convolutional neural networks with global attention for improved materials property prediction (PMID: 32766627)
OpenWaterAnalytics/epanet-dev (⭐64 · C++) Development Repository for the object-oriented implementation of EPANET (PMID: 31096428)
Vini2/phables (⭐64 · Python) 🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes (PMID: 37738590)
ggonnella/gfapy (⭐64 · Python) Gfapy: a flexible and extensible software library for handling sequence graphs in Python (PMID: 28645150)
kimmo1019/DeepCDR (⭐64 · Python) Cancer Drug Response Prediction via a Hybrid Graph Convolutional Network (PMID: 33381841)
lrkrol/SEREEGA (⭐64 · MATLAB) SEREEGA: Simulating Event-Related EEG Activity (PMID: 30114381)
nadeemlab/CEP (⭐64 · Python) Computational Endoscopy Platform (advanced deep learning toolset for analyzing endoscopy videos) [MICCAI'22, MICCAI'21, ISBI'21, CVPR'20] (PMID: 34642595; 35403172; 36178456)
qiyunzhu/woltka (⭐64 · Python) Woltka: a versatile meta'omic data classifier (PMID: 36073806)
tk2/RetroSeq (⭐64 · Perl) RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps. (PMID: 23233656)
tripal/tripal (⭐64 · PHP) The Tripal package is a suite of Drupal modules for creating biological (genomic, genetic, breeding) websites. Visit the Tripal homepage at http://tripal.info for documentation, support, and other information. The Drupal project page is at http://drupal.org/project/tripal. (PMID: 29220446)
ygidtu/trackplot (⭐64 · Python) trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. (PMID: 37669275)
zqgao22/HIGH-PPI (⭐64 · Python) None (PMID: 36841846)
ParkerLab/ataqv (⭐63 · C++) A toolkit for QC and visualization of ATAC-seq results. (PMID: 32213349)
ggonnella/gfaviz (⭐63 · C++) Graphical interactive tool for the visualization of sequence graphs in GFA format. (PMID: 30596893)
ncbi/BAMscale (⭐63 · C) BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods. (PMID: 32321568)
ocxtal/libgaba (⭐63 · C) Adaptive semi-global banded alignment on string graphs (PMID: 29504909)
HALFpipe/HALFpipe (⭐62 · Python) ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data (PMID: 35305030)
MannLabs/ProteomicsVisualization (⭐62 · Jupyter Notebook) This is a collection of minimal code to visualize various aspects of proteomics data. (PMID: 35107884)
WatsonLab/MAGpy (⭐62 · Python) Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie) (PMID: 30418481)
abehr/pong (⭐62 · Python) Fast analysis and visualization of latent clusters in population genetic data (PMID: 27283948)
bcgsc/ntedit (⭐62 · C++) ✏️ Genome assembly polishing & SNV detection (PMID: 31095290; 35567771)
danielhuson/megan-ce (⭐62 · Java) MEGAN Community Edition (PMID: 27327495)
genesofeve/projectR (⭐62 · HTML) None (PMID: 32167521)
hellloxiaotian/ESRGCNN (⭐62 · Python) Image Super-resolution with An Enhanced Group Convolutional Neural Network (Neural Networks, 2022) (PMID: 35779445)
husonlab/megan-ce (⭐62 · Java) MEGAN Community Edition (PMID: 36825821)
nikhilroxtomar/TGANet (⭐62 · Python) TGANet: Text-guided attention for improved polyp segmentation [Early Accepted & Student Travel Award at MICCAI 2022] (PMID: 36780239)
BenoitMorel/GeneRax (⭐61 · C++) None (PMID: 32502238; 35021210)
KailiWang1/DeepDTAF (⭐61 · Jupyter Notebook) a deep learning architecture for protein-ligand binding affinity prediction (PMID: 33834190)
Oshlack/STRetch (⭐61 · Python) Method for detecting STR expansions from short-read sequencing data (PMID: 30129428)
RVanDamme/MUFFIN (⭐61 · Nextflow) hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis (PMID: 33561126)
VCCRI/CIDR (⭐61 · R) Clustering through Imputation and Dimensionality Reduction (PMID: 28351406)
YifanDengWHU/DDIMDL (⭐61 · Python) None (PMID: 32407508)
dewyman/TranscriptClean (⭐61 · Python) Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome (PMID: 29912287)
harbourlab/UPhyloplot2 (⭐61 · Python) Draw phylogenetic trees of tumor evolution (PMID: 34090344)
paiardin/DockingPie (⭐61 · Python) A Consensus Docking Plugin for PyMOL (PMID: 35792827)
BTheDragonMaster/pikachu (⭐60 · Python) Python-based Informatics Kit for Analysing Chemical Units (PMID: 35672769)
KCCG/ClinSV (⭐60 · Perl) Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data (PMID: 33632298)
ablab/viralVerify (⭐60 · Python) viralVerify: viral contig verification tool (PMID: 32413137)
brettc/partitionfinder (⭐60 · Python) PartitionFinder discovers optimal partitioning schemes for DNA sequences. (PMID: 28013191)
dtamayo/spock (⭐60 · Python) 🖖 A package to determine whether planetary orbital configurations will live long and prosper (PMID: 34599094)
griffithlab/pVAC-Seq (⭐60 · Python) DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools (PMID: 26825632)
iprada/Circle-Map (⭐60 · Python) A method for circular DNA detection based on probabilistic mapping of ultrashort reads (PMID: 31830908)
mourisl/Rcorrector (⭐60 · C++) Error correction for Illumina RNA-seq reads (PMID: 26500767)
SAMtoBAM/MUMandCo (⭐59 · Shell) MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation (PMID: 32096823)
SofieVG/FlowSOM (⭐59 · R) Using self-organizing maps for visualization and interpretation of cytometry data (PMID: 25573116)
XiaoTaoWang/HiCLift (⭐59 · Python) A fast and efficient tool for converting chromatin interaction data between genome assemblies (PMID: 37335863)
ksahlin/ultra (⭐59 · Python) Long-read splice alignment with high accuracy (PMID: 34302453)
rhysf/Synima (⭐59 · Perl) Synteny Imager (PMID: 29162056)
volkamerlab/KinFragLib (⭐59 · Jupyter Notebook) Kinase-focused fragment library (PMID: 33155465)
xavierdidelot/TransPhylo (⭐59 · R) Reconstruction of transmission trees using genomic data (PMID: 28100788)
ymcui/expmrc (⭐59 · Python) ExpMRC: Explainability Evaluation for Machine Reading Comprehension (PMID: 35497046)
Genotek/ClassifyCNV (⭐58 · Python) ClassifyCNV: a tool for clinical annotation of copy-number variants (PMID: 33230148)
NBISweden/EMBLmyGFF3 (⭐58 · Python) An efficient way to convert gff3 annotation files into EMBL format ready to submit. (PMID: 30103816)
RyanCook94/inphared (⭐58 · Perl) Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines. (PMID: 36159887)
SRKH/S4NN (⭐58 · Jupyter Notebook) Temporal backpropagation for spiking neural networks with one spike per neuron, by S. R. Kheradpisheh and T. Masquelier, International Journal of Neural Systems (2020), doi: 10.1142/S0129065720500276 (PMID: 32466691)
dantaki/SV2 (⭐58 · Python) Support Vector Structural Variation Genotyper (PMID: 29300834)
eliberis/parapred (⭐58 · Python) Paratope Prediction using Deep Learning (PMID: 29672675)
haifangong/TRFE-Net-for-thyroid-nodule-segmentation (⭐58 · Python) [ISBI'21, CBM'22] TRFE-Net for thyroid nodule segmentation (PMID: 36812810)
materialsintelligence/matscholar (⭐58 · Python) Code to access the Matscholar public API. (PMID: 31361962)
telatin/BamToCov (⭐58 · Nim) 🏔 coverage extraction from BAM/CRAM files, supporting targets 📊 (PMID: 35199151)
10XGenomics/scHLAcount (⭐57 · TeX) Count HLA alleles in single-cell RNA-seq data (PMID: 32330223)
OpenNFT/OpenNFT (⭐57 · MATLAB) OpenNFT is an integrated software package designed for neurofeedback training and automatic real-time fMRI quality assessment (rtQA). (PMID: 28795112)
Proteomicslab57357/UniprotR (⭐57 · R) Retrieving Information of Proteins from Uniprot (PMID: 31843688)
QuKunLab/ATAC-pipe (⭐57 · Python) Analysis pipeline for ATAC-seq Data (PMID: 29982337)
bene51/3Dscript (⭐57 · Java) Create 3D/4D animations using a natural language-based syntax (PMID: 34152405)
cyang03/CHECKED (⭐57 · Jupyter Notebook) None (PMID: 34178179)
jltsiren/gbwt (⭐57 · C++) Substring index for paths in a graph (PMID: 31406990)
ksahlin/BESST (⭐57 · Python) BESST - scaffolder for genomic assemblies (PMID: 27153683)
lczech/gappa (⭐57 · C++) A toolkit for analyzing and visualizing phylogenetic (placement) data (PMID: 30169747; 32016344)
nitzanlab/biolord (⭐57 · Python) None (PMID: 38225466)
rnacentral/R2DT (⭐57 · PostScript) Visualise RNA secondary structure in consistent, reproducible and recognisable layouts (PMID: 34108470)
rundherum/pymia (⭐57 · Python) pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis (PMID: 33137700)
Data2Dynamics/d2d (⭐56 · MATLAB) a modeling environment tailored to parameter estimation in dynamical systems (PMID: 32176768)
JhuangLab/BioInstaller (⭐56 · R) A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform (PMID: 30402350)
PapenfussLab/bioshake (⭐56 · Haskell) Bioinformatics pipelines with Haskell and Shake (PMID: 31328031)
RuleWorld/bionetgen (⭐56 · Perl) Rule-based modeling framework (PMID: 27402907)
ddofer/ProFET (⭐56 · Python) ProFET: Protein Feature Engineering Toolkit for Machine Learning (PMID: 26130574)
eskederks/eMAGMA-tutorial (⭐56 · None) A step by step guide on how to use eMAGMA, an approach to conducting eQTL informed gene-based tests. (PMID: 33624746)
giannimonaco/ABIS (⭐56 · R) None (PMID: 30726743)
jpquast/protti (⭐56 · R) Picotti lab data analysis package. (PMID: 36699412)
lcnhappe/happe (⭐56 · Matlab) Harvard Automated Pre-Processing Pipeline for EEG (PMID: 29535597)
lczech/genesis (⭐56 · C++) A library for working with phylogenetic and population genetic data. (PMID: 32016344)
niemasd/ViralMSA (⭐56 · Python) Reference-guided multiple sequence alignment of viral genomes (PMID: 32814953)
twestbrookunh/paladin (⭐56 · C) Protein Alignment and Detection Interface (PMID: 28158639)
vembrane/vembrane (⭐56 · Python) vembrane filters VCF records using python expressions (PMID: 36519840)
PacificBiosciences/HiPhase (⭐55 · Rust) Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads (PMID: 38269623)
aehrc/cvt2distilgpt2 (⭐55 · Python) Improving Chest X-Ray Report Generation by Leveraging Warm-Starting (PMID: 37783533)
baranwa2/Struct2Graph (⭐55 · Python) A PyTorch implementation of GCN with mutual attention for protein-protein interaction prediction (PMID: 36088285)
biocore/gneiss (⭐55 · Jupyter Notebook) compositional data analysis toolbox (PMID: 28144630)
gtonkinhill/fastbaps (⭐55 · R) A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data (PMID: 31076776)
hillerlab/GenomeAlignmentTools (⭐55 · C) Tools for improving the sensitivity and specificity of genome alignments (PMID: 31742600)
immunedynamics/spectre (⭐55 · HTML) A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. (PMID: 33840138)
jag1g13/pycgtool (⭐55 · Python) Generate coarse-grained molecular dynamics models from atomistic trajectories. (PMID: 28345910)
muellan/metacache (⭐55 · C++) memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping (PMID: 28961782)
pratas/cryfa (⭐55 · C++) A secure encryption tool for genomic data (PMID: 30020420)
smfleming/HMeta-d (⭐55 · MATLAB) Hierarchical meta-d' model (PMID: 29877507)
tjhwangxiong/TCGAplot (⭐55 · R) A number of functions were generated to perform pan-cancer DEG analysis, correlation analysis between gene expression and TMB, MSI, TIME, and promoter methylation. Methods for visualization were provided in order to easily perform integrative pan-cancer multi-omics analysis. (PMID: 38105215)
vibbits/phyd3 (⭐55 · JavaScript) Phylogenetic tree viewer based on D3.js (PMID: 28525531)
xq141839/DCSAU-Net (⭐55 · Python) Elsevier-CIBM-2023: A deeper and more compact split-attention U-Net for medical image segmentation (PMID: 36736096)
RealityBending/Pyllusion (⭐54 · Python) A Parametric Framework to Generate Visual Illusions using Python (PMID: 34841973)
UCLOrengoGroup/cath-tools (⭐54 · C++) Protein structure comparison tools such as SSAP and SNAP (PMID: 30295745)
acadTags/Explainable-Automated-Medical-Coding (⭐54 · Python) Implementation and demo of explainable coding of clinical notes with Hierarchical Label-wise Attention Networks (HLAN) (PMID: 33711543)
alfonsosemeraro/pyplutchik (⭐54 · Python) Python visualisation for Plutchik annotated corpora. (PMID: 34469455)
charite/jannovar (⭐54 · Java) Annotation of VCF variants with functional impact and from databases (executable+library) (PMID: 24677618)
dayoonkwon/BioAge (⭐54 · R) Biological Age Calculations Using Several Biomarker Algorithms (PMID: 34725754)
insilichem/pychimera (⭐54 · Python) Use UCSF Chimera Python API in a standard interpreter (PMID: 29340616)
kiharalab/DOVE (⭐54 · Python) A Deep-learning based dOcking decoy eValuation mEthod (PMID: 31746961)
lasigeBioTM/MER (⭐54 · Shell) Minimal Named-Entity Recognizer (MER) (PMID: 30519990)
luoyuanlab/Clinical-Longformer (⭐54 · Python) None (PMID: 36451266)
minoh0201/DeepMicro (⭐54 · Python) Deep representation learning for disease prediction based on microbiome data (PMID: 32265477)
mlbendall/telescope (⭐54 · Python) Quantification of transposable element expression using RNA-seq (PMID: 31568525)
mlin/spVCF (⭐54 · C++) Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently (PMID: 33300997)
morispi/CONSENT (⭐54 · C++) Scalable long read self-correction and assembly polishing with multiple sequence alignment (PMID: 33436980)
sequencing/NxTrim (⭐54 · C++) Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries. (PMID: 25661542)
stevemussmann/admixturePipeline (⭐54 · Python) A pipeline that accepts a VCF file to run through Admixture (PMID: 32727359; 38046098)
tanghaibao/quota-alignment (⭐54 · Python) Guided synteny alignment between duplicated genomes (within specified quota constraint) (PMID: 21501495)
ushaham/BatchEffectRemoval (⭐54 · Python) None (PMID: 28419223)
xiaoyeye/GCNG (⭐54 · Python) using graph convolutional neural network and spaital transcriptomics data to infer cell-cell interactions (PMID: 33303016)
BioinfoUNIBA/REDItools (⭐53 · Python) REDItools are python scripts to investigate RNA editing at genomic scale. (PMID: 31996844)
HannesStark/protein-localization (⭐53 · Jupyter Notebook) Using Transformer protein embeddings with a linear attention mechanism to make SOTA de-novo predictions for the subcellular location of proteins 🔬 (PMID: 36700108)
JLSteenwyk/PhyKIT (⭐53 · Python) a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies (PMID: 33560364)
KirillKryukov/naf (⭐53 · C) Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences (PMID: 30799504)
MolecularAI/Icolos (⭐53 · Python) Icolos: A workflow manager for structure based post-processing of de novo generated small molecules (PMID: 36073898)
RASpicer/MetabolomicsTools (⭐53 · None) None (PMID: 28890673)
RWilton/Arioc (⭐53 · None) Arioc: GPU-accelerated DNA short-read alignment (PMID: 25780763; 29554207)
clwgg/nQuire (⭐53 · C) A statistical framework for ploidy estimation using NGS short-read data (PMID: 29618319)
hkaneko1985/dcekit (⭐53 · Python) DCEKit (Data Chemical Engineering toolKit) (PMID: 35309472; 37360490; 38496944)
kamimrcht/REINDEER (⭐53 · C++) REINDEER REad Index for abuNDancE quERy (PMID: 32657392)
maickrau/MBG (⭐53 · C++) None (PMID: 33475133)
oxpig/DEVELOP (⭐53 · Python) None (PMID: 34881010)
sigven/cpsr (⭐53 · R) Cancer Predisposition Sequencing Reporter (CPSR) (PMID: 34310709)
songweizhi/MetaCHIP (⭐53 · Python) Horizontal gene transfer (HGT) identification pipeline (PMID: 30832740)
theislab/AutoGeneS (⭐53 · Jupyter Notebook) None (PMID: 34293324)
theislab/trvae (⭐53 · Python) Conditional out-of-distribution prediction (PMID: 33381839)
zhangxaochen/CuFusion (⭐53 · C++) None (PMID: 28974030)
zhaoxiaofei/BinDash (⭐53 · C++) Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop (PMID: 30052763)
AChavignon/PALA (⭐52 · MATLAB) Sharing scripts and functions for OPUS-PALA article, and LOTUS Software. All functions are usable with agreement from their owner. (PMID: 35177778)
BojarLab/glycowork (⭐52 · Jupyter Notebook) Package for processing and analyzing glycans and their role in biology. (PMID: 34192308; 38708029)
BorgwardtLab/S3M (⭐52 · C++) A software package for statistically significant shapelet mining (PMID: 29949972; 33381811)
CBIIT/LDlinkR (⭐52 · R) LDlinkR (PMID: 32180801)
PedroMTQ/mantis (⭐52 · Python) A package to annotate protein sequences (PMID: 34076241)
WGLab/bioformer (⭐52 · None) Bioformer: an efficient BERT model for biomedical text mining (PMID: 36945685)
choderalab/ensembler (⭐52 · Python) Automated omics-scale protein modeling and simulation setup. (PMID: 27337644)
cramerlab/warp (⭐52 · C#) None (PMID: 31591575)
daquang/YAMDA (⭐52 · Python) Yet Another Motif Discovery Algorithm (PMID: 29790915)
frankMusacchia/Annocript (⭐52 · Perl) Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript (PMID: 25701574)
irycisBioinfo/PATO (⭐52 · R) PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species. (PMID: 34623430)
kassonlab/gmxapi (⭐52 · C++) (outdated) fork of https://gitlab.com/gromacs/gromacs (PMID: 29912282)
kundajelab/dfim (⭐52 · Python) Deep Feature Interaction Maps (DFIM) (PMID: 30423062)
mrazvan22/brain-coloring (⭐52 · Python) BrainPainter - Brain Visualisation Software (PMID: 33537683)
noriakis/CBNplot (⭐52 · R) Bayesian network plot for the enrichment analysis results (PMID: 35561164)
nygenome/conpair (⭐52 · Python) Concordance and contamination estimator for tumor–normal pairs (PMID: 27354699)
psipred/cgdms (⭐52 · Python) Differentiable molecular simulation of proteins with a coarse-grained potential (PMID: 34473813)
ETHmodlab/BIMODAL (⭐51 · Python) Supporting code for the paper "Bidirectional Molecule Generation with Recurrent Neural Networks" (J. Chem. Inf. 2020, 60, 3). (PMID: 31904964)
MolecularAI/Lib-INVENT (⭐51 · Jupyter Notebook) None (PMID: 34460269)
TheJacksonLaboratory/SVE (⭐51 · Python) None (PMID: 29559002)
chopralab/lemon (⭐51 · C++) A framework for rapidly mining structural information from the Protein Data Bank (PMID: 30873531; 32639154)
edawson/gfakluge (⭐51 · C++) A C++ library and utilities for manipulating the Graphical Fragment Assembly format. (PMID: 31535074)
insilicomedicine/BiAAE (⭐51 · Python) Molecular Generation for Desired Transcriptome Changes with Adversarial Autoencoders (PMID: 32362822)
mstsuite/MuST (⭐51 · Fortran) Multiple Scattering Theory code for first principles calculations (PMID: 33344416)
ncclabsustech/DeepSeparator (⭐51 · Python) Deep learning model for EEG artifact removal (PMID: 35378524)
psathyrella/partis (⭐51 · C++) B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction (PMID: 26751373; 31329576; 33175831)
BigDataBiology/macrel (⭐50 · Python) Predict AMPs in (meta)genomes and peptides (PMID: 33384902)
Merck/Matcher (⭐50 · Python) Matcher is a tool for understanding how chemical structure optimization problems have been solved. Matcher enables deep control over searching structure/activity relationships (SAR) derived from large datasets, and takes the form of an accessible web application with simple deployment. Matcher is built around the mmpdb platform. (PMID: 36977316)
aldro61/kover (⭐50 · Python) Learn interpretable computational phenotyping models from k-merized genomic data (PMID: 27671088)
compbiomed/animalcules (⭐50 · R) R shiny app for interactive microbiome analysis (PMID: 33775256)
fgcz/rawrr (⭐50 · R) Access Orbitrap data in R lang using C# mono assembly - bioconductor package (PMID: 33686856)
hosseinshn/MOLI (⭐50 · Jupyter Notebook) MOLI: Multi-Omics Late Integration with deep neural networks for drug response prediction (PMID: 31510700)
nadeemlab/Physics-ArX (⭐50 · Python) Physics-based data augmentation library for quantifying CT and CBCT images in radiotherapy [PMB'23, PMB'21, Medical Physics'21, AAPM'21] (PMID: 34245012)
pachterlab/metakallisto (⭐50 · Python) Using kallisto for metagenomic analysis (PMID: 28334086)
precimed/mixer (⭐50 · C) Causal Mixture Model for GWAS summary statistics (PMID: 32539089)
rcs333/VAPiD (⭐50 · Shell) VAPiD: Viral Annotation and Identification Pipeline (PMID: 30674273)
schmeing/ReSeq (⭐50 · C++) More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original (PMID: 33608040)
stephaniehicks/qsmooth (⭐50 · R) Smooth quantile normalization (qsmooth) is a generalization of quantile normalization, which is an average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups. (PMID: 29036413)
HaploKit/vechat (⭐49 · C++) Correcting errors in noisy long reads using variation graphs (PMID: 36333324)
IBM/fold2seq (⭐49 · Python) Code for Fold2Seq paper from ICML 2021 (PMID: 34423306)
IFMlab/ChemFlow (⭐49 · Python) Computational Chemistry Workflows (PMID: 36603846; 37620503)
JLiangLab/BenchmarkTransferLearning (⭐49 · Python) Official PyTorch Implementation and Pre-trained Models for Benchmarking Transfer Learning for Medical Image Analysis (PMID: 35713581)
LaboratorioBioinformatica/MARVEL (⭐49 · Python) MARVEL: Metagenomic Analyses and Retrieval of Viral ELements (PMID: 30131825)
XiaoweiXu/ImageCAS-A-Large-Scale-Dataset-and-Benchmark-for-Coronary-Artery-Segmentation-based-on-CT (⭐49 · None) None (PMID: 37634975)
algbio/themisto (⭐49 · C++) Space-efficient pseudoalignment with a colored de Bruijn graph (PMID: 37387143)
biopragmatics/biomappings (⭐49 · Jupyter Notebook) 🗺️ Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. (PMID: 36916735)
brentp/hts-nim-tools (⭐49 · Nim) useful command-line tools written to showcase hts-nim (PMID: 29718142)
gbouras13/plassembler (⭐49 · Python) Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates (PMID: 37369026)
horsepurve/DeepRTplus (⭐49 · Python) Deep (Transfer) Learning for Peptide Retention Time Prediction (PMID: 30114359)
marbl/harvest (⭐49 · None) None (PMID: 25410596)
msproteomicstools/msproteomicstools (⭐49 · Python) Some hopefully useful tools for mass spectrometry applied to proteomics (PMID: 25788625)
perishky/meffil (⭐49 · HTML) Efficient algorithms for analyzing DNA methylation data. (PMID: 29931280)
soedinglab/wish (⭐49 · C++) Predict prokaryotic host for phage metagenomic sequences (PMID: 28957499)
stephenslab/flashr (⭐49 · R) R package for Empirical Bayes Factor Analysis. (PMID: 37920532)
wenqi006/SlideGraph (⭐49 · Python) None (PMID: 35640384)
willtownes/nsf-paper (⭐49 · Jupyter Notebook) Nonnegative spatial factorization for multivariate count data (PMID: 36587187)
yvquanli/trimnet (⭐49 · Python) Code for paper "TrimNet: learning molecular representation from triplet messages for biomedicine " (PMID: 33147620)
ADicksonLab/wepy (⭐48 · Python) Weighted Ensemble simulation framework in Python (PMID: 33344813)
CSUBioGroup/DeepPPISP (⭐48 · Python) Protein-protein interaction sites prediction through combining local and global features with deep neural networks (PMID: 31593229)
ChuHan89/WSSS-Tissue (⭐48 · Python) None (PMID: 35671591)
ELELAB/mutatex (⭐48 · Python) scripts and facilities for in-silico mutagenesis with FoldX (PMID: 35323860)
MannLabs/alphapeptstats (⭐48 · Jupyter Notebook) Python Package for the downstream analysis of mass-spectrometry-based proteomics data (PMID: 37527012)
PayamDiba/SERGIO (⭐48 · Python) A simulator for single-cell expression data guided by gene regulatory networks (PMID: 32871105)
PingChang818/TDSTF (⭐48 · Python) None (PMID: 38350189)
VCCRI/Sierra (⭐48 · R) Discover differential transcript usage from polyA-captured single cell RNA-seq data (PMID: 32641141)
alanqrwang/keymorph (⭐48 · Python) Robust multimodal brain registration via keypoints (PMID: 37769550)
arttumiettinen/pi2 (⭐48 · C++) C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster. (PMID: 31116382)
bcgsc/orca (⭐48 · R) 🐳 Genomics Research Container Architecture (PMID: 31004474)
hongwang01/InDuDoNet (⭐48 · Python) 【MICCAI 2021】An Interpretable Dual Domain Network for CT Metal Artifact Reduction (PMID: 36623381)
jyangfsu/WQChartPy (⭐48 · Python) Python Package for Visualization of Water Geochemistry Data (PMID: 35157303)
sigven/oncoEnrichR (⭐48 · R) Cancer-dedicated gene set interpretation (PMID: 37551617)
yuzhimanhua/lm-lstm-crf (⭐48 · None) None (PMID: 30307536)
AnantharamanLab/ViWrap (⭐47 · Python) A wrapper to identify, bin, classify, and predict host-viral relationship for viruses (PMID: 38152703)
BimberLab/DISCVRSeq (⭐47 · HTML) A collection of command line tools for working with sequencing data (PMID: 31309221)
IARCbioinfo/needlestack (⭐47 · R) Multi-sample somatic variant caller (PMID: 32363341)
KlugerLab/t-SNE-Heatmaps (⭐47 · R) Beta version of 1D t-SNE heatmaps to visualize expression patterns of hundreds of genes simultaneously in scRNA-seq (PMID: 30742040)
OHNLP/MedTator (⭐47 · JavaScript) A Serverless Text Annotation Tool for Corpus Development (PMID: 34983060)
UnixJunkie/FASMIFRA (⭐47 · Python) Molecular Generation by Fast Assembly of SMILES Fragments (PMID: 34775976)
andreped/NoCodeSeg (⭐47 · Jupyter Notebook) 🔬 Code-free deep segmentation for computational pathology (PMID: 35155486)
blackrim/treePL (⭐47 · C++) Phylogenetic penalized likelihood (PMID: 22908216)
ignaciorlando/red-lesion-detection (⭐47 · MATLAB) This code implements a red lesion detection method based on a combination of hand-crafted features and CNN based descriptors. Our paper is under revision now, so please do not use this repository until we release the paper. (PMID: 29157445)
joshr17/IFM (⭐47 · Python) Code for paper "Can contrastive learning avoid shortcut solutions?" NeurIPS 2021. (PMID: 35546903)
lmdu/dockey (⭐47 · Python) an integrated tool for molecular docking and virtual screening (PMID: 36764832)
rinikerlab/Ensembler (⭐47 · Python) Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method development or to deepen understanding of a broad spectrum of modeling methods, from basic sampling techniques to enhanced sampling and free energy calculations. It is easy to install, fast, increases shareability, comparability, and reproducibility of scientific code developments. (PMID: 33512157)
rothlab/chromozoom (⭐47 · JavaScript) ChromoZoom is a fast, fluid web-based genome browser (PMID: 23220575)
variani/lme4qtl (⭐47 · R) Mixed models @lme4 + custom covariances + parameter constraints (PMID: 29486711)
yfukai/laptrack (⭐47 · Python) Particle tracking by solving linear assignment problem. (PMID: 36495181)
BioinfoUNIBA/REDItools2 (⭐46 · Python) None (PMID: 32838738)
LooseLab/bulkvis (⭐46 · Python) None (PMID: 30462145)
blaxterlab/blobology (⭐46 · Perl) Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED) (PMID: 24348509)
bobeobibo/phigaro (⭐46 · HTML) Phigaro is a scalable command-line tool for predicting phages and prophages (PMID: 32311023)
citiususc/BigSeqKit (⭐46 · Go) BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale (PMID: 37522758)
dmnfarrell/epitopepredict (⭐46 · Jupyter Notebook) Python package and command line tool for epitope prediction (PMID: 36824339)
genomicsITER/NanoDJ (⭐46 · Jupyter Notebook) NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly (PMID: 31072312)
kshulgina/codetta (⭐46 · Python) None (PMID: 36511586)
lanagarmire/cox-nnet (⭐46 · Python) None (PMID: 29634719)
liutairan/eMolFrag (⭐46 · Python) eMolFrag is a molecular fragmentation tool based on BRICS algorithm written in Python. (PMID: 28346786)
microsoft/RespireNet (⭐46 · Python) This is the official implementation of the work RespireNet. (PMID: 34891348)
mpcrlab/MolecularTransformerEmbeddings (⭐46 · Jupyter Notebook) Code and data for the Transformer neural network trained to translate between molecular text representations and create molecular embeddings. (PMID: 32568539)
quxiaojian/PGA (⭐46 · Perl) Plastid Genome Annotator (PMID: 31139240)
shilpagarg/WHdenovo (⭐46 · Python) None (PMID: 31860070)
stephenslab/rss (⭐46 · MATLAB) Regression with Summary Statistics. (PMID: 29399241)
wgmao/PLIER (⭐46 · R) Pathway-Level Information Extractor (PLIER): a generative model for gene expression data (PMID: 31249421)
CDCgov/datasets-sars-cov-2 (⭐45 · Perl) Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/) (PMID: 36093336)
PoonLab/covizu (⭐45 · JavaScript) Rapid analysis and visualization of coronavirus genome variation (PMID: 37124703)
SmartDataAnalytics/BioKEEN (⭐45 · Jupyter Notebook) A computational library for learning and evaluating biological knowledge graph embeddings - please see the main PyKEEN repo at https://github.com/pykeen/pykeen/ (PMID: 30768158)
ZJUYH/radar-to-lidar-place-recognition (⭐45 · Python) Radar-to-Lidar: Heterogeneous Place Recognition via Joint Learning (PMID: 34079825)
andreasmang/claire (⭐45 · C++) Constrained Large Deformation Diffeomorphic Image Registration (CLAIRE) (PMID: 35295546)
aquaskyline/LRSIM (⭐45 · C) 10x Genomics Reads Simulator (PMID: 29213995)
boxiangliu/ParaMed (⭐45 · Python) Chinese to English medical translation (PMID: 34488734)
duolinwang/MusiteDeep (⭐45 · Python) MusiteDeep provides a deep-learning method for general and kinase-specific phosphorylation site prediction. It is implemented by deep learning library Keras and Theano backend (the Keras2.0 and Tensorflow backend implementation were also provided under folder MusiteDeep_Keras2.0). At present, MusiteDeep only provides prediction of human phosphorylation sites; however, it also provides customized model training that enables users to train other PTM prediction models by using their own training data sets based on either CPU or GPU. (PMID: 29036382; 32324217)
flatironinstitute/inferelator (⭐45 · Python) Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network. (PMID: 35188184)
gerberlab/mitre (⭐45 · Python) The Microbiome Interpretable Temporal Rule Engine (PMID: 31477162)
jordisr/poreover (⭐45 · Python) Nanopore basecalling and consensus decoding (PMID: 33468205)
keiserlab/LUNA (⭐45 · Jupyter Notebook) None (PMID: 36102784)
msraredon/NICHES (⭐45 · HTML) Niche Interactions and Cellular Heterogeneity in Extracellular Signaling (PMID: 36458905)
petmri/ROCKETSHIP (⭐45 · MATLAB) Dynamic Contrast Enhanced (DCE) MRI Analysis Software (PMID: 26076957)
phipsonlab/speckle (⭐45 · R) R package for analysing single cell data (PMID: 36005887)
qingyuzhao/br-net (⭐45 · Jupyter Notebook) None (PMID: 33243992)
schallerdavid/pyrod (⭐45 · Python) PyRod - Tracing water molecules in molecular dynamics simulations (PMID: 31117512)
svalkiers/clusTCR (⭐45 · Python) CDR3 clustering module providing a new method for fast and accurate clustering of large data sets of CDR3 amino acid sequences, and offering functionalities for downstream analysis of clustering results. (PMID: 34132766)
thomas0809/RxnScribe (⭐45 · Jupyter Notebook) A Sequence Generation Model for Reaction Diagram Parsing (PMID: 37368970)
vlothec/TRASH (⭐45 · R) RepeatIdentifier (PMID: 37162382)
yijingru/ANCIS-Pytorch (⭐45 · Python) [Medical Image Analysis 2019] Attentive Neural Cell Instance Segmentation (PMID: 31103790)
BackofenLab/IntaRNA (⭐44 · C++) Efficient target prediction incorporating accessibility of interaction sites (PMID: 30590479)
CancerDataScience/NuCLS (⭐44 · Jupyter Notebook) NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation (PMID: 34586355)
GATB/simka (⭐44 · C++) Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets. (PMID: 31504187)
LightersWang/Awesome-Active-Learning-for-Medical-Image-Analysis (⭐44 · Python) [MedIA] Accompanying paper list and source code for survey "A comprehensive survey on deep active learning in medical image analysis" (PMID: 38776841)
LouisFaure/scFates (⭐44 · Python) a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data. (PMID: 36394263)
LyonsLab/coge (⭐44 · Perl) CoGe (Comparative Genomics) Platform (PMID: 28334338; 29474529)
MedChaabane/deepRAM (⭐44 · Python) End-to-end deep learning toolkit for predicting protein binding sites and motifs. (PMID: 31510640)
TheJacksonLaboratory/Picky (⭐44 · Perl) Structural Variants Pipeline for Long Reads (PMID: 29713081)
YuSugihara/MutMap (⭐44 · Python) MutMap pipeline to identify causative mutations responsible for a phenotype (PMID: 35321412)
caiyu6666/DDAD-ASR (⭐44 · Python) [MedIA'2023] Dual-distribution discrepancy with self-supervised refinement for anomaly detection in medical images (PMID: 36934507)
evidenceontology/evidenceontology (⭐44 · HTML) Evidence & Conclusion Ontology development site: Use ISSUES to request terms. See WIKI for how to request terms. See README for how to cite ECO. Visit our website for more project info. (PMID: 34986598)
guopengf/FL-MRCM (⭐44 · Python) Multi-institutional Collaborations for Improving Deep Learning-based Magnetic Resonance Image Reconstruction Using Federated Learning (PMID: 35444379)
kdmurray91/kwip (⭐44 · C++) De novo estimates of genetic relatedness from next-gen sequencing data (PMID: 28873405)
kundajelab/ChromDragoNN (⭐44 · Jupyter Notebook) Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts" (PMID: 31510655)
leylabmpi/Struo (⭐44 · Jupyter Notebook) Ley Lab MetaGenome Profiler DataBase generator (PMID: 31778148)
lmweber/cytometry-clustering-comparison (⭐44 · R) R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data (PMID: 27992111)
meddwl/psearch (⭐44 · Python) 3D ligand-based pharmacophore modeling (PMID: 30486389)
nluhmann/BlastFrost (⭐44 · C++) None (PMID: 33430919)
oddt/rfscorevs (⭐44 · Jupyter Notebook) RF-Score-VS - Random forest based protein-ligand scoring function for Virtual Screening (PMID: 28440302)
psipred/DeepCov (⭐44 · Python) Fully convolutional neural networks for protein residue-residue contact prediction (PMID: 29718112)
wyang17/SQuIRE (⭐44 · Python) Software for Quantifying Interspersed Repeat Expression (PMID: 30624635)
YuSugihara/QTL-seq (⭐43 · Python) QTL-seq pipeline to identify causative mutations responsible for a phenotype (PMID: 35321412)
ablab/TandemTools (⭐43 · C++) Tool for assessing/improving assembly quality in extra-long tandem repeats (PMID: 32657355)
brentp/combined-pvalues (⭐43 · Python) combining p-values using modified stouffer-liptak for spatially correlated results (probes) (PMID: 22954632)
cellgeni/batchbench (⭐43 · R) None (PMID: 33524142)
ctlab/GADMA (⭐43 · Python) Genetic Algorithm for Demographic Model Analysis (PMID: 32112099)
foxlf823/Multi-Filter-Residual-Convolutional-Neural-Network (⭐43 · Python) Multi-Filter Residual Convolutional Neural Network for Text Classification (PMID: 34322282)
idruglab/hignn (⭐43 · Jupyter Notebook) Code for "HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention" (PMID: 36519623)
ikalatskaya/ISOWN (⭐43 · Perl) None (PMID: 28659176)
josuebarrera/GenEra (⭐43 · Shell) genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families. (PMID: 36964572)
mahmoodlab/HistoFL (⭐43 · Python) Federated Learning for Computational Pathology - Medical Image Analysis (PMID: 34911013)

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