Single Cell Genomics Python Packages

tiledbsoma

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

squidpy

Spatial Single Cell Analysis in Python

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

palantir

Single cell trajectory detection

crested

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

brisc

Fast single-cell toolkit

snapatac2

Single-cell epigenomics analysis tools

cellrank

CellRank: dynamics from multi-view single-cell data

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

cytome

Single-file format for single-cell multi-omics and spatial transcriptomics — matrices, metadata, embeddings, fragments and provenance in one SQLite-backed .cytome file, with SQL metadata queries and genomic range indexes.

scxpand

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

scarches

Reference mapping for single-cell genomics

piaso-mcp

Agent-neutral knowledge hub that makes the PIASO single-cell omics ecosystem (PIASO, COSG/COSGR, LARIS, Emergene, PIASOmarkerDB) first-class for any coding agent. One canonical source generates Claude skills, Cursor rules, AGENTS.md, llms.txt, and an MCP server.

vsparse

Store and analyze scRNAseq data with extreme memory efficiency.

scvi

Deep probabilistic analysis of single-cell and spatial omics data

scxpand-cuda

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

scgen

Single cell perturbation prediction

truecell

Pure-Python port of Seurat (v5) — single-cell RNA-seq and spatial transcriptomics analysis (Xenium/Visium/CosMx), built on NumPy/SciPy/AnnData.

scmalignantfinder

scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells from their normal counterparts.

awgan

Codes for paper: AWGAN: A Powerful Batch Effect Removal Model for scRNA-seq Data

sctour

A deep learning architecture for robust inference and accurate prediction of cellular dynamics

singlecellhaystack

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

roma-analysis

Representation and Quantification Of Module Activity in Single Cells