All repos — GH Trending Explorer

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 skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.

Dong-Fang-Bu-Bai / btr-dualrag

Source code for BTR-dualRAG: Bioinformatics Tool Recommendation With Dual Retrieval-Augmented Generation

mehek-builds / Entry-Level-Computational-Biology-Bioinformatics-Jobs

Entry level computational biology, bioinformatics, biostatistics and biotech data science jobs and internships, from employers' own job boards. Rebuilt every Monday. Maintained by Litos.

Developer-Y / cs-video-courses

List of Computer Science courses with video lectures.

plotly / dash

Data Apps & Dashboards for Python. No JavaScript Required.

biopython / biopython

Official git repository for Biopython (originally converted from CVS)

danielecook / Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

synthetic-sciences / openscience

The open-source AI workbench for scientific research

seandavi / awesome-single-cell

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

google / deepvariant

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

nextflow-io / nextflow

A workflow language for data-driven computational pipelines

sokrypton / ColabFold

Making Protein folding accessible to all!

scverse / scanpy

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

OpenGene / fastp

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

soedinglab / MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

ai4s-research / awesome-ai-for-science

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

broadinstitute / gatk

Official code repository for GATK versions 4 and up

bioconda / bioconda-recipes

Conda recipes for the bioconda channel.

galaxyproject / galaxy

Data intensive science for everyone.

rust-bio / rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

shenwei356 / seqkit

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

MultiQC / MultiQC

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

K-Dense-AI / k-dense-byok

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

omicverse / omicverse

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

scikit-bio / scikit-bio

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

a-r-j / graphein

Protein Graph Library

shenwei356 / csvtk

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

ClawBio / ClawBio

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

sib-swiss / training-collection

Collection of bioinformatics training materials

shenwei356 / rush

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

broadinstitute / cromwell

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

hail-is / hail

Cloud-native genomic dataframes and batch computing

xuzhougeng / wisp-science

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

beita6969 / ScienceClaw

Verifiable program-level self-evolution for AI-for-Science agents: Skills and typed Operators grow from replay-verified executions.

biotite-dev / biotite

A comprehensive library for computational molecular biology

samtools / htslib

C library for high-throughput sequencing data formats

COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

pysam-developers / pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

bacalhau-project / bacalhau

Community-driven, simple, yet powerful framework for fast, cost-effective distributed Compute over Data.

danforthcenter / plantcv

Plant phenotyping with image analysis

BenLangmead / bowtie2

A fast and sensitive gapped read aligner

scverse / anndata

Annotated data.

deeptools / deepTools

Tools to process and analyze deep sequencing data.

scverse / PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

torognes / vsearch

Versatile open-source tool for microbiome analysis

BioPandas / biopandas

Working with molecular structures in pandas DataFrames

zaeleus / noodles

Bioinformatics I/O libraries in Rust

OpenChemistry / avogadrolibs

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing

datavzrd / datavzrd

A tool to create visual HTML reports from collections of CSV/TSV tables

aaryansamanta / ai-research-publications

High-school research portfolio: 2 peer-reviewed publications (IEEE, IJHSR) + 3 active projects spanning quantum-inspired ML, computational biology, biomedical imaging, wildfire RL, and science-education research. Stanford Medicine, UCLA COSMOS & UCSB SRA affiliated.