#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.

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

Pure-Rust reader for Thermo Fisher .raw mass-spectrometry files, with Python bindings.

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

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