Single Cell Python Packages

tiledbsoma

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

decoupler

Python package to perform enrichment analysis from omics data.

anndata2ri

Convert between AnnData and SingleCellExperiment

vitessce

Python API and Jupyter widget for Vitessce

liana

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

celltypist

A tool for semi-automatic cell type classification

omicverse

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

pyscenic

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

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

mellon

Non-parametric density inference for single-cell analysis.

pertpy

Single-cell perturbation analysis

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

rustscenic

Rust and PyO3 implementation of SCENIC-style single-cell regulatory-network analysis. GRN, AUCell, topics, cisTarget, peak calling, cell QC, enhancer-gene links, and eRegulon assembly in one pip install.

cirrocumulus

Bring your single-cell data to life

velocyto

RNA velocity estimation in Python

scgpt

Large-scale generative pretrain of single cell using transformer.

allcools

Toolkit for single-cell DNA methylation analysis.

infercnvpy

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

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

scvelo-rs

Drop-in Rust + PyO3 acceleration of scvelo for single-cell RNA velocity

trisicell

No description available

scarches

Reference mapping for single-cell genomics

pyvia

trajectory inference

rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis