Single Cell Python Packages

tiledbsoma

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

mellon

Non-parametric density inference for single-cell analysis.

decoupler

Python package to perform enrichment analysis from omics data.

marsilea

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

liana

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

celltypist

A tool for semi-automatic cell type classification

brisc

Fast single-cell toolkit

velocyto

RNA velocity estimation in Python

phate

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

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

infercnvpy

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

singlecellexperiment

Container class for single-cell experiments

vitessce

Python API and Jupyter widget for Vitessce

pertpy

Single-cell perturbation analysis

scdataset

scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics

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.

scarf

Memory-efficient single-cell analysis in Python. Stream RNA, ATAC, CITE-seq and multi-omics from local or remote Zarr stores, from laptop to atlas scale, with reusable fingerprinted results.

omicverse

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

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

allcools

Toolkit for single-cell DNA methylation analysis.

cirrocumulus

Bring your single-cell data to life

polariseq

Atlas-scale single-cell RNA-seq analysis in Python with a Rust core. Plans memory before reading; runs in memory or out of core.

spatioloji-s

Python toolkit for image-based spatial transcriptomics (CosMx, MERFISH, Xenium). Unified data object for expression, polygons, and FOV images, plus QC, clustering, point- and polygon-based spatial statistics, and polygon-native cell-cell communication using real membrane contact geometry.

crispyx

crispyx is a Python package for scalable CRISPR and Perturb-seq screen analysis on disk-backed AnnData files. It provides streaming quality control, normalization, pseudobulk aggregation, and differential expression without loading the full count matrix into memory.