scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

omicverse / omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

scverse / gget

🧬 gget enables efficient querying of genomic reference databases

deeptools / deepTools

Tools to process and analyze deep sequencing data.

scverse / PyDESeq2

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

cafferychen777 / mLLMCelltype

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

scverse / squidpy

Spatial Single Cell Analysis in Python

aristoteleo / dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

windmirrorai / nanomirrors

State-of-the-art bio cell models for inference and training. Minimal, readable, and produciton-ready.