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

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

A tool for semi-automatic cell type classification

Graph-linked unified embedding for single-cell multi-omics data integration

DANCE: a deep learning library and benchmark platform for single-cell analysis

Single cell perturbation prediction

rapids-singlecell: GPU-accelerated framework for scRNA analysis

Single-cell perturbation analysis

LIANA+: an all-in-one framework for cell-cell communication

Python package to perform enrichment analysis from omics data.

Multi-omic single-cell optimal transport tools

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

RNA velocity estimation in Python

scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks

Deep neural networks for predicting CpG methylation

Convert between AnnData and SingleCellExperiment

Tools for single-cell data processing

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.

A tool for semi-automatic cell type harmonization and integration