Scverse Python Packages

anndata

Annotated data.

scanpy

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

scverse-misc

Miscellaneous utility code used by scverse packages

mudata

Multimodal Data (.h5mu) implementation for Python

spatialdata

An open and interoperable data framework for spatial omics data

squidpy

Spatial Single Cell Analysis in Python

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

decoupler

Python package to perform enrichment analysis from omics data.

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.

muon

muon is a multimodal omics Python framework

scib-metrics

Accelerated, Python-only, single-cell integration benchmarking metrics

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

infercnvpy

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

snapatac2

Single-cell epigenomics analysis tools

pertpy

Single-cell perturbation analysis

scirpy

A scanpy extension to analyse single-cell TCR and BCR data.

lazyslide

Accessible and interoperable whole slide image analysis for digital pathology in Python

pylimma

Python port of R limma for differential expression analysis

alphapepttools

Search- and quantification-engine agnostic biological interpretation of proteomics data

rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

ehrapy

Electronic Health Record Analysis with Python.

rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

scvi

Deep probabilistic analysis of single-cell and spatial omics data

pyclustree

A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.