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scverse
scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

77K 2K 447
scverse
squidpy

Spatial Single Cell Analysis in Python

43K 567 114
saezlab
liana

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

28K 283 32
gmrukwa
divik

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

15K 14 6
theislab
cellrank

CellRank: dynamics from multi-view single-cell data

9K 443 57
pachterlab
kb-python

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

4K 187 29
jkobject
scdataloader

a dataloader to work with large single cell datasets from lamindb

2K 40 6
YosefLab
scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 447
parashardhapola
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.

2K 115 15
yizhak-lab-ccg
scxpand

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

2K 8 4
cbg-ethz
scdef

Deep exponential families for single-cell data.

2K 20 1
theislab
sccoda

A Bayesian model for compositional single-cell data analysis

2K 195 27
trytoolchest
toolchest-client

Python client for Toolchest

2K 15 0
yizhak-lab-ccg
scxpand-cuda

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

1K 8 4
genecell
piaso-tools

Precise Integrative Analysis of Single-cell Omics.

1K 6 2
bodegalab
irescue

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

988 22 3
gao-lab
cell-blast

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

925 94 13
MaxMLang
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.

817 0 0
KevinMenden
scaden

Deep Learning based cell composition analysis with Scaden.

657 90 31
deweylab
cello-classify

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

613 68 14
Ashford-A
scope-bio

scOPE learns mutation-linked expression programs from bulk RNA-seq and projects them into single-cell RNA-seq to infer per-cell mutation probabilities, revealing subclonal evolutionary structure that complements CNV analyses.

606 1 0
TheOmarLab
sctrial

Participant-level differential analysis for longitudinal single-cell experiments: DiD, paired comparisons, module scoring, pseudobulk, and power analysis.

591 2 0
jonyyqn
scmalignantfinder

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

583 18 3
Risitop
transmorph

A unifying data integration framework.

578 11 2
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