scverse/rapids-singlecell

Single-cell analysis in Python. Scales to >100M cells.

Deep probabilistic analysis of single-cell and spatial omics data

Single-cell perturbation analysis

R toolkit for single cell genomics

Single-cell epigenomics analysis tools

Spatial Single Cell Analysis in Python

10x Genomics Single Cell Analysis

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

Community-provided extensions to Seurat