Single Cell Python Packages

anndata2ri

Convert between AnnData and SingleCellExperiment

tiledbsoma

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

decoupler

Python package to perform enrichment analysis from omics data.

celltypist

A tool for semi-automatic cell type classification

liana

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

vitessce

Python API and Jupyter widget for Vitessce

mellon

Non-parametric density inference for single-cell analysis.

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.

omicverse

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

pertpy

Single-cell perturbation analysis

phate

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

autozyme

Autonomous multi-agent framework to optimize scientific software

infercnvpy

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

velocyto

RNA velocity estimation in Python

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

cellestial

An Interactive and Highly Customizable Single-Cell and Spatial Biology Plotting Library

scgpt

Large-scale generative pretrain of single cell using transformer.

checkatlas

One liner tool to check the quality of your single-cell atlases.

bonesistools

Python-implemented toolkits for upstream and downstream analyses around the BoNesis ecosystem.

cirrocumulus

Bring your single-cell data to life

allcools

Toolkit for single-cell DNA methylation analysis.

moscot

Multi-omic single-cell optimal transport tools

rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

scarches

Reference mapping for single-cell genomics