#bioinformatics

Official git repository for Biopython (originally converted from CVS)

A structural variation pipeline for short-read sequencing

rapids-singlecell: GPU-accelerated framework for scRNA analysis

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

viral-ngs: command line tools and wrappers for processing raw viral genomic data

C library for high-throughput sequencing data formats

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 170,000+ scientists worldwide. 158 ready-to-use 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.

A comprehensive library for computational molecular biology

BioMCP: Biomedical Model Context Protocol

Cloud-native genomic dataframes and batch computing

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.

A scientific plotting library in Rust

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

Search ClinicalTrials.gov trials, retrieve study details and results, and match patients to eligible trials via MCP. STDIO or Streamable HTTP.

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

A Rust-based, headless workflow execution framework supporting local, cloud, and HPC.

SemiBin: metagenomics binning with self-supervised deep learning

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

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

The Pharmacogenomic Clinical Annotation Tool

Cell type annotation for single-cell RNA-seq using multi-LLM consensus