Scverse Python Packages

anndata

Annotated data.

scanpy

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

mudata

Multimodal Data (.h5mu) implementation for Python

scvi-tools

Deep probabilistic analysis of single-cell and spatial 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

pertpy

Single-cell perturbation analysis

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

infercnvpy

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

ehrapy

Electronic Health Record Analysis with Python.

scvi

Deep probabilistic analysis of single-cell and spatial omics data

pyclustree

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

rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

treedata

anndata with trees

grnndata

Awesome GRN enhanced AnnData toolkit

pytximport

Feature-rich Python implementation of the tximport package for gene count estimation.

spatiomic

A Python package for unsupervised analysis of spatial (prote)omics data.

pylimma

Python port of R limma for differential expression analysis

metaspace-converter

Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData

alphapepttools

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

pycea-lineage

scverse lineage tracing analysis toolkit

chame

Chromatin analysis module

gedi2py

A high-performance Python package for single-cell genomics