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

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.

Detection tandem repeat variations (TR-CNVs) and structural variations (SVs) using long reads

Scaling Single Cell Analysis to Millions of Cells

Probabilistic cell segmentation for in situ spatial transcriptomics

Efficient, parallel compression for terabyte-scale data

LLM inference in C/C++

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