#bioinformatics

Python package to perform enrichment analysis from omics data.

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

Official git repository for Biopython (originally converted from CVS)

rapids-singlecell: GPU-accelerated framework for scRNA analysis

A visualization grammar and GPU-accelerated toolkit for genomic data

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 190,000+ scientists worldwide. 165 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.

A structural variation pipeline for short-read sequencing

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

BioMCP: Biomedical Model Context Protocol

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

A universal toolkit for upstream processing of long RNA reads

A plotly.js React component from Plotly 📈

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

A comprehensive library for computational molecular biology

Cloud-native genomic dataframes and batch computing

Unified research-data acquisition MCP — search & fetch datasets across Zenodo, DataCite, NCBI omics (GEO/SRA/BioProject), and literature (PubMed/OpenAIRE) behind one normalized model.

C library for high-throughput sequencing data formats

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

A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.

📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

The Chemistry Development Kit

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

Gene Set Enrichment Analysis in Python