Single Cell Python Packages

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.

liana

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

anndata2ri

Convert between AnnData and SingleCellExperiment

vitessce

Python API and Jupyter widget for Vitessce

celltypist

A tool for semi-automatic cell type classification

omicverse

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

mellon

Non-parametric density inference for single-cell analysis.

phate

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

pertpy

Single-cell perturbation analysis

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

scgpt

Large-scale generative pretrain of single cell using transformer.

velocyto

RNA velocity estimation in Python

pyvia

trajectory inference

cirrocumulus

Bring your single-cell data to life

allcools

Toolkit for single-cell DNA methylation analysis.

infercnvpy

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

scarches

Reference mapping for single-cell genomics

trisicell

No description available

scatac-fragment-tools

Tools for working with scATAC-seq fragment files

moscot

Multi-omic single-cell optimal transport tools

scdiffeq

Learn single-cell dynamics using neural differential equations

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis