scverse/squidpy

Deep probabilistic analysis of single-cell and spatial omics data

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

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

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

Annotated data.

R toolkit for single cell genomics

Histology Spatial Topology for Omics Profiling and Inter-section Alignment

RNA Velocity generalized through dynamical modeling

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.