Python package for isoform resolution analysis based on long-read RNA-seq data

An extensible and performant aligner and read mapper

An interactive explorer for single-cell transcriptomics data

A curated list of awesome genomics and bioinformatics agentic skills, MCPs and benchmarks for Claude Code, Copilot, Codex, Cursor, Gemini CLI, etc

DoWhy is a Python library for causal inference that supports explicit modeling and testing of causal assumptions. DoWhy is based on a unified language for causal inference, combining causal graphic…

Phylogenetic orthology inference for comparative genomics

Variational autoencoder for metagenomic binning

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

Multiple Protein Structure Alignment at Scale with FoldMason

The official pipeline for flexible and high-performance analysis of DNBelab C Serie single-cell data.

A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. Stored as pure Python. All in a modern, AI-native editor.

Specification and documentation for Agent Skills

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

RNA velocity inference for single cell and spatial data

Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

Whole Genome Alignment Tools

Collection of mRNA benchmarks

Democratizing AI scientists with ToolUniverse

Minimalist Async Evaluation Framework for R

A GTF-native ORF annotation tool for transcriptomes

A tool for exploring large trees in the browser

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

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

Assembly and binning of metagenomes

The Book of Statistical Proofs

An extremely fast Python package and project manager, written in Rust.

R bindings to libarchive, supporting a large variety of archive formats