Most popular bioinformatics repositories and open source projects

cs-video-courses Developer-Y

List of Computer Science courses with video lectures.

84.5k 11.6k 2k

scientific-agent-skills K-Dense-AI Python

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 250,000+ scientists worldwide. 177 ready-to-use validated ski...

56k 4.9k 210

dash plotly Python

Data Apps & Dashboards for Python. No JavaScript Required.

24.5k 2.3k 422

open-science aipoch TypeScript

The open-source AI research workbench for scientific research and agent workflows. Local-first, model-agnostic desktop app with extensible skills, MCP...

5.4k 551 224

biopython biopython Python

Official git repository for Biopython (originally converted from CVS)

5.3k 2k 163

Awesome-Bioinformatics danielecook

A curated list of awesome Bioinformatics libraries and software.

4.4k 749 167

openscience synthetic-sciences TypeScript

The open-source AI workbench for scientific research

4.3k 546 19

awesome-single-cell seandavi

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

3.9k 1.1k 237

deepvariant google Python

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

3.8k 808 156

nextflow nextflow-io Groovy

A workflow language for data-driven computational pipelines

3.5k 821 81

ColabFold sokrypton Jupyter Notebook

Making Protein folding accessible to all!

3k 757 59

scanpy scverse Python

Single-cell analysis in Python. Scales to >100M cells.

2.6k 808 50

fastp OpenGene C++

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

2.5k 389 48

minimap2 lh3 C

A versatile pairwise aligner for genomic and spliced nucleotide sequences

2.3k 484 81

MMseqs2 soedinglab C

MMseqs2: ultra fast and sensitive search and clustering suite

2.2k 314 26

awesome-ai-for-science ai4s-research

A curated list of awesome AI tools, libraries, papers, datasets, and frameworks that accelerate scientific discovery — from physics and chemistry to b...

2.1k 261 16

medical-research-skills aipoch Python

Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.

2k 200 62

gatk broadinstitute Java

Official code repository for GATK versions 4 and up

2k 631 155

scispacy allenai Python

A full spaCy pipeline and models for scientific/biomedical documents.

2k 259 44

galaxy galaxyproject Python

Data intensive science for everyone.

1.9k 1.2k 61

bioconda-recipes bioconda Shell

Conda recipes for the bioconda channel.

1.9k 4.2k 88

bwa lh3 C

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

1.8k 580 105

seqkit shenwei356 Go

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

1.6k 191 26

seqtk lh3 C

Toolkit for processing sequences in FASTA/Q formats

1.6k 333 61

MultiQC MultiQC JavaScript

Aggregate results from bioinformatics analyses across many samples into a single report.

1.5k 696 31

k-dense-byok K-Dense-AI TypeScript

An AI co-scientist running on your desktop. Claude Science but better.

1.4k 189 8

getting-started-with-genomics-tools-and-resources crazyhottommy Shell

Unix, R and python tools for genomics and data science

1.4k 363 87

omicverse omicverse Python

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

1.4k 151 9

foldseek steineggerlab C

Foldseek enables fast and sensitive comparisons of large structure sets.

1.3k 164 20

TDC mims-harvard Jupyter Notebook

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

1.3k 228 29

scikit-bio scikit-bio Python

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

1.3k 363 53

graphein a-r-j Jupyter Notebook

Protein Graph Library

1.2k 147 16

DeepPurpose kexinhuang12345 Jupyter Notebook

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

1.2k 307 28

deep_gcns_torch lightaime Python

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

1.2k 152 14

ClawBio ClawBio Python

🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.

1.2k 292 15

csvtk shenwei356 Go

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

1.2k 94 20

rush shenwei356 Go

A cross-platform command-line tool for executing jobs in parallel

1.1k 69 20

pyCirclize moshi4 Python

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

1.1k 66 10

scipipe scipipe Go

Robust, flexible and resource-efficient pipelines using Go and the commandline

1.1k 74 32

react-plotly.js plotly JavaScript

A plotly.js React component from Plotly 📈

1.1k 138 42

ncbi-genome-download kblin Python

Scripts to download genomes from the NCBI FTP servers

1.1k 180 32

cromwell broadinstitute Scala

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environme...

1.1k 383 106

hail hail-is Python

Cloud-native genomic dataframes and batch computing

1.1k 267 49

wisp-science xuzhougeng Rust

Open-source, local-first desktop AI research workbench for scientific computing with Python/R, MCP bioinformatics tools, SSH/WSL/GPU runtimes, and Ope...

1.1k 108 3