An extension of NumPyro for first-class support of dynamical systems.

fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector

An experimental library for metaprogramming with algebraic effects and handlers

MAS-Iso-Seq Isoform Identification and Quantification

Pairwise whole genome aligner

VACmap: a long-read aligner specifically designed for complex structural variation discovery

Single Rust: Pioneering single-cell analysis with Rust's concurrency for scalable, high-throughput pipelines. 🧬🚀

Probabilistic model of RNA velocity

A local-haplotagging-based small and structural variant caller

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

Genotyping of copy number sensitive allele-specific haplotypes

A list of software for pangenomics

Piecewise alignment for layers of mosaics

MMseqs2: ultra fast and sensitive search and clustering suite

Image processing in Python

Sparse Lazy Array Format (SLAF) for Single-Cell Genomics

State is a machine learning model that predicts cellular perturbation response across diverse contexts

Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration

ONEcode package to replace SAM/BAM, especially for eDNA mapping to everything

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

Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)

Deep learning at the speed of light.