Single Cell Rna Seq Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

95K 2K 450

squidpy

Spatial Single Cell Analysis in Python

56K 569 113

liana

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

19K 287 33

cellrank

CellRank: dynamics from multi-view single-cell data

10K 447 57

divik

Divisive Intelligent K-Means algorithm (DiviK) for joint feature selection and clustering of heavily multidimensional data.

8K 14 6

kb-python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

3K 188 30

scvelo-rs

Drop-in Rust + PyO3 acceleration of scvelo for single-cell RNA velocity

3K 12 0

scdataloader

a dataloader to work with large single cell datasets from lamindb

3K 40 7

scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 450

toolchest-client

Toolchest Python client

2K 15 0

sccoda

A Bayesian model for compositional single-cell data analysis

2K 196 27

scdef

Deep exponential families for single-cell data.

1K 20 1

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

1K 116 15

scxpand

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

1K 8 4

irescue

Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq

1K 22 3

cell-blast

Single-cell transcriptome querying tool

1K 94 13

scmalignantfinder

scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells from their normal counterparts.

924 19 3

scxpand-cuda

Pan-cancer detection of T-cell clonal expansion from single-cell RNA sequencing (CUDA-enabled)

803 8 4

cxg-census-mcp

MCP server for CZ CELLxGENE Discover Census. Single-cell RNA-seq queries, ontology-aware (CL, UBERON, EFO), provenance-tracked. For Claude, Cursor, MCP clients.

781 0 0