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

infercnvpy

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

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

pyclustree

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

rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

scvi

Deep probabilistic analysis of single-cell and spatial omics data

ehrapy

Electronic Health Record Analysis with Python.

treedata

anndata with trees

grnndata

Awesome GRN enhanced AnnData toolkit

pytximport

pytximport is Python implementation of `tximport` to transform transcript counts from transcriptome mapping tools into gene count estimations.

metaspace-converter

Convert Metaspace datasets to AnnData

scsplice

Single-cell alternative-splicing analysis

spatiomic

A python toolbox for spatial omics analysis.

alphapepttools

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

pylimma

Python port of R limma for differential expression analysis

pycea-lineage

Scverse lineage tracing toolkit

gedi2py

Gene Expression Decomposition for Integration - scverse-compliant single-cell RNA-seq batch correction