domain: bioinformatics
118 products, primary matches first, then adoption-weighted; health v2 shown.
| Product | Health v2 | Stars | Maturity |
|---|---|---|---|
| K-Dense-AI/scientific-agent-skills A library of 163 validated Agent Skills plus integrations with 100+ scientific databases that turn AI coding agents into scientific researc… | 79 | 34724 | active |
| cytoscape/cytoscape.js Cytoscape.js is a fully featured graph theory (network) library written in pure JavaScript for modelling, analysing, and visualising relati… | 99 | 11188 | stable |
| google-deepmind/alphafold3 Google DeepMind's official implementation of the AlphaFold 3 inference pipeline for predicting biomolecular structures and interactions. It… | 83 | 8495 | active |
| deepchem/deepchem DeepChem is a Python library that democratizes deep learning for drug discovery, quantum chemistry, materials science, and biology. It prov… | 67 | 6961 | active |
| biopython/biopython Biopython is a widely used open-source Python library of tools for computational molecular biology and bioinformatics. It provides modules … | 76 | 5176 | stable |
| attractivechaos/klib Klib is a standalone, lightweight C library of generic data structures and algorithms implemented largely as single-header files using C ma… | 58 | 4717 | stable |
| jwohlwend/boltz Boltz is a family of open-source biomolecular interaction models (Boltz-1 and Boltz-2) that predict complex structures and binding affiniti… | 63 | 4177 | active |
| ArcInstitute/evo2 Evo 2 is a DNA foundation language model (1B-40B parameters) that models genomes at single-nucleotide resolution with up to 1 million base … | 62 | 4157 | active |
| google/deepvariant DeepVariant is a deep learning-based genomic variant caller that converts aligned DNA sequencing reads (BAM/CRAM) into pileup image tensors… | 70 | 3791 | stable |
| snap-stanford/Biomni Biomni is a general-purpose biomedical AI agent from Stanford that autonomously executes research tasks across biomedical subfields. It com… | 71 | 3790 | active |
| rdkit/rdkit RDKit is an open-source cheminformatics toolkit written in C++ with Python, Java, C#, and JavaScript wrappers. It provides core data struct… | 98 | 3565 | stable |
| google-deepmind/alphafold Open-source implementation of the AlphaFold 2 inference pipeline for predicting protein structures from amino acid sequences, including Alp… | 58 | 14811 | maintenance |
| nextflow-io/nextflow Nextflow is an open-source DSL and runtime for building scalable, portable, and reproducible data-driven computational pipelines, based on … | 97 | 3475 | stable |
| aqlaboratory/openfold OpenFold is a faithful, trainable PyTorch reproduction of DeepMind's AlphaFold 2 for protein structure prediction. It is memory-efficient a… | 48 | 3420 | active |
| openworm/OpenWorm OpenWorm is an open-source project building a comprehensive bottom-up computational model of the Caenorhabditis elegans roundworm, integrat… | 81 | 3037 | active |
| RosettaCommons/RFdiffusion RFdiffusion is an open-source method for de novo protein structure generation using diffusion models, with or without conditional informati… | 62 | 3026 | active |
| Biohub/esm A Python library and model release providing ESMC protein language models, ESMFold2 structure prediction, and the ESM Atlas of 6.8 billion … | 74 | 2927 | active |
| sokrypton/ColabFold ColabFold is a set of tools and Google Colab notebooks that make protein structure prediction with AlphaFold2, AlphaFold3, ESMFold, and rel… | 92 | 2889 | active |
| snakemake/snakemake Snakemake is a Python-based workflow management system for creating reproducible and scalable data analyses. Workflows are defined via a re… | 95 | 2853 | stable |
| satijalab/seurat Seurat is an R toolkit for single-cell genomics developed by the Satija Lab, providing a complete pipeline for analyzing single-cell RNA-se… | 92 | 2790 | stable |
| google-deepmind/science-skills A collection of agent skills from Google DeepMind that extend AI coding agents with structured instructions, scripts, and references for sc… | 74 | 2772 | active |
| scverse/scanpy Scanpy is a scalable Python toolkit for analyzing single-cell gene expression data, built alongside the anndata data structure. It provides… | 93 | 2548 | stable |
| OpenGene/fastp fastp is an ultra-fast all-in-one FASTQ preprocessing and quality control tool written in C++. It handles adapter trimming, quality filteri… | 94 | 2422 | stable |
| neuropsychology/NeuroKit NeuroKit2 is a Python library for neurophysiological and biosignal processing, offering easy access to advanced routines for signals like E… | 80 | 2332 | active |
| MouseLand/cellpose Cellpose is a generalist deep learning algorithm for cellular and nucleus segmentation in microscopy images, with human-in-the-loop capabil… | 86 | 2331 | active |
| RosettaCommons/RoseTTAFold RoseTTAFold is the official implementation of a deep learning system for predicting protein structures and interactions using a three-track… | 23 | 2258 | stable |
| lh3/minimap2 minimap2 is a fast, versatile pairwise sequence aligner for genomic and spliced (RNA-seq) nucleotide sequences, written in C. It maps long … | 76 | 2242 | stable |
| alexdobin/STAR STAR (Spliced Transcripts Alignment to a Reference) is a fast, splice-aware aligner for RNA-seq reads written in C++. It aligns reads to a … | 28 | 2241 | active |
| soedinglab/MMseqs2 MMseqs2 is an open-source C++ suite for ultra-fast, sensitive search and clustering of huge protein and nucleotide sequence sets, running o… | 70 | 2131 | active |
| bytedance/Protenix Protenix is an open-source PyTorch reproduction of AlphaFold 3 for high-accuracy biomolecular structure prediction, covering proteins, nucl… | 79 | 2038 | active |
| broadinstitute/gatk GATK (Genome Analysis Toolkit) is the Broad Institute's industry-standard toolkit for analyzing high-throughput DNA and RNA sequencing data… | 88 | 1991 | active |
| allenai/scispacy scispaCy is a Python library providing full spaCy pipelines, models, and custom pipes for processing scientific, biomedical, and clinical t… | 54 | 1988 | active |
| chaidiscovery/chai-lab Chai-1 is a state-of-the-art multi-modal foundation model for biomolecular structure prediction, handling proteins, small molecules, DNA, R… | 65 | 1986 | active |
| google-deepmind/alphagenome A Python SDK providing programmatic access to Google DeepMind's AlphaGenome model, which predicts genomic regulatory outputs such as gene e… | 89 | 1979 | active |
| openmm/openmm OpenMM is a high-performance toolkit and library for molecular dynamics simulation, with optimized GPU-accelerated kernels. It can be used … | 95 | 1960 | stable |
| samtools/samtools SAMtools is a suite of C command-line programs, built on HTSlib, for reading, writing, editing, indexing, sorting, and viewing SAM/BAM/CRAM… | 96 | 1945 | stable |
| galaxyproject/galaxy Galaxy is an open-source, web-based platform for accessible, reproducible, and transparent data-intensive scientific research, primarily in… | 94 | 1841 | stable |
| rust-bio/rust-bio Rust-Bio is a Rust library providing implementations of algorithms and data structures useful for bioinformatics, such as sequence alignmen… | 90 | 1837 | stable |
| dauparas/ProteinMPNN ProteinMPNN is a PyTorch-based tool that designs amino acid sequences for given protein backbone structures using a message-passing neural … | 23 | 1834 | stable |
| aipoch/medical-research-skills A curated library of 550+ SKILL.md-compatible agent skills for medical and biomedical research, covering evidence insights, protocol design… | 71 | 1763 | active |
| schrodinger/pymol-open-source The open-source foundation of PyMOL, a molecular visualization system for rendering and analyzing 3D structures of proteins, nucleic acids,… | 75 | 1733 | active |
| lucidrains/alphafold3-pytorch A PyTorch implementation of Google DeepMind's Alphafold 3 model for protein and molecular structure prediction. It is a research-oriented r… | 68 | 1691 | active |
| scverse/scvi-tools scvi-tools is a Python library for deep probabilistic modeling and analysis of single-cell and spatial omics data, built on PyTorch, PyTorc… | 93 | 1681 | stable |
| MDAnalysis/mdanalysis MDAnalysis is an open-source Python library for analyzing molecular dynamics simulations of many-body systems at the molecular scale. It re… | 74 | 1637 | stable |
| bowang-lab/scGPT scGPT is a foundation model for single-cell multi-omics built with a generative transformer, providing pretrained checkpoints and a Python … | 67 | 1620 | active |
| shenwei356/seqkit SeqKit is an ultrafast, cross-platform command-line toolkit written in Go for manipulating FASTA and FASTQ sequence files, offering 38+ sub… | 81 | 1590 | active |
| DeepGraphLearning/torchdrug TorchDrug is a PyTorch-based machine learning library for drug discovery, covering graph neural networks, deep generative models, and reinf… | 23 | 1587 | active |
| gcorso/DiffDock DiffDock is a deep learning implementation of a diffusion generative model for molecular docking, predicting how small molecule ligands bin… | 31 | 1569 | active |
| evo-design/evo Evo is a 7-billion-parameter DNA foundation model built on the StripedHyena architecture, trained on ~300 billion tokens of prokaryotic who… | 71 | 1560 | active |
| lh3/seqtk Seqtk is a fast, lightweight C command-line toolkit for processing sequences in FASTA and FASTQ formats, with optional gzip support and onl… | 34 | 1559 | stable |
| jokergoo/ComplexHeatmap An R/Bioconductor package for creating complex heatmaps with flexible arrangement of multiple heatmaps and rich annotation graphics. It is … | 57 | 1536 | active |
| ANTsX/ANTs Advanced Normalization Tools (ANTs) is a C++ command-line library for high-dimensional medical image registration and segmentation, built o… | 83 | 1497 | active |
| MultiQC/MultiQC MultiQC is a Python command-line tool that scans directories for log files and outputs from 150+ bioinformatics tools and aggregates them i… | 88 | 1489 | stable |
| qupath/qupath QuPath is an open-source desktop application for bioimage analysis, aimed especially at digital pathology and whole-slide imaging. It provi… | 79 | 1430 | active |
| imagej/imagej2 ImageJ2 is an open-source Java framework and application for processing and analyzing N-dimensional scientific image data, built on the Img… | 75 | 1399 | stable |
| openbabel/openbabel Open Babel is an open-source chemical toolbox that reads, writes, converts, searches, and analyzes chemical data across more than 100 molec… | 92 | 1376 | stable |
| quiltdata/quilt Quilt is a scientific data management platform built on AWS that turns S3 data into deeply versioned, metadata-rich data packages for teams… | 67 | 1370 | active |
| nextstrain/ncov A Nextstrain build pipeline that analyzes SARS-CoV-2 viral genomes to understand their evolution and spread, producing phylogenetic visuali… | 88 | 1363 | active |
| ncbi/sra-tools The NCBI SRA Toolkit is a collection of command-line tools and libraries for accessing, converting, and downloading data from the INSDC Seq… | 77 | 1362 | active |
| nf-core/rnaseq nf-core/rnaseq is a Nextflow-based bioinformatics pipeline for analyzing RNA sequencing data, performing QC, trimming, (pseudo-)alignment w… | 94 | 1357 | active |
| google/neuroglancer Neuroglancer is a WebGL-based, client-side web application for visualizing large 3-D volumetric datasets, supporting arbitrary cross-sectio… | 77 | 1355 | active |
| vgteam/vg vg is a C++ toolkit for building, manipulating, and analyzing genome variation graphs (pangenome graphs). It provides succinct graph data s… | 94 | 1333 | active |
| agemagician/ProtTrans ProtTrans provides state-of-the-art pre-trained Transformer language models for protein sequences, trained on thousands of GPUs and hundred… | 33 | 1324 | active |
| bbuchfink/diamond DIAMOND is a BLAST-compatible local sequence aligner for protein and translated DNA searches, designed for high-performance analysis of lar… | 97 | 1316 | active |
| steineggerlab/foldseek Foldseek is a command-line tool for fast and sensitive comparison, search, and clustering of large protein 3D structure sets, including mon… | 67 | 1283 | active |
| microsoft/BioGPT BioGPT is Microsoft's domain-specific generative Transformer language model pre-trained on biomedical text, with implementation code and pr… | 32 | 4488 | maintenance |
| stardist/stardist StarDist is a Python library for object detection and instance segmentation in 2D and 3D microscopy images using star-convex shapes, built … | 60 | 1255 | stable |
| scikit-bio/scikit-bio scikit-bio is an open-source, BSD-licensed Python library providing data structures, algorithms, and educational resources for bioinformati… | 86 | 1229 | active |
| YuLab-SMU/clusterProfiler An R/Bioconductor package for functional enrichment analysis (ORA, GSEA, topology-aware) of omics data across thousands of species. It prov… | 76 | 1226 | active |
| martinpacesa/BindCraft BindCraft is a Python-based computational pipeline for de novo protein binder design that combines AlphaFold2 backpropagation, ProteinMPNN,… | 78 | 1196 | active |
| scverse/gget gget is a free, open-source Python package and command-line tool for efficiently querying genomic reference databases such as Ensembl, UniP… | 92 | 1195 | active |
| facebookresearch/esm Meta FAIR's Evolutionary Scale Modeling (ESM) library providing Transformer protein language models with pretrained weights, including ESM-… | 10 | 4170 | maintenance |
| omicverse/omicverse OmicVerse is a Python library for multi-omics analysis covering bulk, single-cell, and spatial RNA-seq workflows. It is part of the scverse… | 94 | 1193 | active |
| a-r-j/graphein Graphein is a Python library for constructing graph and mesh representations of proteins, RNA, molecules, and biological interaction networ… | 76 | 1190 | active |
| shenwei356/csvtk csvtk is a cross-platform command-line toolkit written in Go for manipulating CSV/TSV tabular data. It provides many subcommands for filter… | 86 | 1169 | active |
| deepmodeling/Uni-Mol Uni-Mol is a collection of 3D molecular representation learning frameworks and pretrained models for tasks like molecule property predictio… | 34 | 1155 | active |
| ScorpioLea/AiCE AiCE is a Python tool that predicts high-fitness protein mutations by sampling sequences from protein inverse folding models such as Protei… | 40 | 1144 | active |
| paulvangentcom/heartrate_analysis_python HeartPy is a Python library for analyzing heart rate from PPG (photoplethysmography) and ECG signals, including noisy and low-resolution we… | 49 | 1137 | active |
| CellProfiler/CellProfiler CellProfiler is a free, open-source desktop application for quantitative analysis of biological images, letting biologists build modular im… | 68 | 1135 | active |
| shenwei356/rush rush is a cross-platform command-line tool written in Go for executing jobs in parallel, similar to GNU parallel. It supports custom variab… | 73 | 1132 | active |
| K-Dense-AI/k-dense-byok K-Dense BYOK is a free, open-source desktop application providing 'Kady', an AI research assistant (co-scientist) that runs locally and use… | 78 | 1126 | active |
| ClawBio/ClawBio ClawBio is a bioinformatics-native AI agent skill library offering 97 curated, reproducible skills for genomics tasks like pharmacogenomics… | 81 | 1123 | active |
| WojciechMula/pyahocorasick A Python module (implemented as a C extension with a pure-Python fallback) implementing the Aho-Corasick algorithm for fast multi-pattern s… | 76 | 1120 | stable |
| PaddlePaddle/PaddleHelix PaddleHelix is a bio-computing platform built on PaddlePaddle featuring large-scale representation learning and multi-task deep learning fo… | 57 | 1119 | active |
| moshi4/pyCirclize pyCirclize is a Python package built on matplotlib for creating circular visualizations such as Circos plots, chord diagrams, and radar cha… | 72 | 1113 | active |
| opensim-org/opensim-core OpenSim Core is a C++ library and set of command-line applications for building musculoskeletal models and running dynamic simulations of m… | 86 | 1105 | stable |
| PharMolix/OpenBioMed OpenBioMed is an open-source toolkit and agent platform for biomedicine and life science, offering multimodal models like BioMedGPT-Mol, 45… | 72 | 1103 | active |
| xuzhougeng/wisp-science Wisp Science is an open-source, local-first desktop AI research workbench that combines an LLM agent with persistent Python/R kernels, MCP-… | 81 | 1087 | active |
| SimpleITK/SimpleITK SimpleITK is a simplified C++ interface to the Insight Toolkit (ITK) for multi-dimensional image analysis, including filtering, segmentatio… | 98 | 1084 | stable |
| kblin/ncbi-genome-download A Python command-line tool for downloading bacterial, fungal, viral, and other genome files from NCBI's FTP servers in GenBank, FASTA, and … | 57 | 1083 | active |
| broadinstitute/cromwell Cromwell is an open-source Workflow Management System from the Broad Institute that executes scientific workflows written in WDL (Workflow … | 80 | 1080 | active |
| CJ-Chen/TBtools-II TBtools-II is a stand-alone bioinformatics platform with a user-friendly GUI and command-line tools for analyzing high-throughput sequencin… | 92 | 1074 | active |
| broadinstitute/picard Picard is a set of Java command line tools from the Broad Institute for manipulating high-throughput sequencing data in formats such as SAM… | 85 | 1074 | stable |
| hail-is/hail Hail is an open-source Python library for scalable exploration and analysis of genomic data, built on Spark, Scala, and C++ primitives for … | 91 | 1070 | active |
| ccsb-scripps/AutoDock-Vina AutoDock Vina is an open-source molecular docking engine used for predicting how small molecules bind to protein targets. It supports fast … | 73 | 1062 | active |
| bigdatagenomics/adam ADAM is a genomics analysis platform built on Apache Spark that provides schemas and APIs for processing genomic data like reads, variants,… | 55 | 1057 | active |
| wu-yc/LabClaw LabClaw is a modular library of 240 SKILL.md agent skills for biomedical AI research, covering biology, drug discovery, medicine, data scie… | 48 | 1048 | active |
| arq5x/bedtools2 bedtools is a suite of command-line utilities for genome arithmetic, enabling set-theory operations like intersect, merge, count, complemen… | 62 | 1045 | stable |
| HannesStark/boltzgen BoltzGen is an open-source all-atom generative diffusion model for designing protein and peptide binders against arbitrary biomolecular tar… | 71 | 1042 | active |
| cBioPortal/cbioportal cBioPortal is an open-source web application for visualization, analysis, and download of large-scale cancer genomics datasets. This reposi… | 97 | 1032 | active |
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