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Single Cell Rna Seq Python Packages

Python packages with the GitHub topic single-cell-rna-seq. Sorted by relevance, with stars and monthly downloads.
scverse
scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

95K 2K 450
scverse
squidpy

Spatial Single Cell Analysis in Python

56K 569 113
saezlab
liana

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

19K 287 33
theislab
cellrank

CellRank: dynamics from multi-view single-cell data

10K 447 57
gmrukwa
divik

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

8K 14 6
pachterlab
kb-python

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

3K 188 30
ilaykav
scvelo-rs

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

3K 12 0
jkobject
scdataloader

a dataloader to work with large single cell datasets from lamindb

3K 40 7
YosefLab
scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 450
trytoolchest
toolchest-client

Toolchest Python client

2K 15 0
theislab
sccoda

A Bayesian model for compositional single-cell data analysis

2K 196 27
cbg-ethz
scdef

Deep exponential families for single-cell data.

1K 20 1
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.

1K 116 15
yizhak-lab-ccg
scxpand

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

1K 8 4
bodegalab
irescue

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

1K 22 3
gao-lab
cell-blast

Single-cell transcriptome querying tool

1K 94 13
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.

924 19 3
yizhak-lab-ccg
scxpand-cuda

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

803 8 4
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.

781 0 0
deweylab
cello-classify

CellO

759 68 14
lueckenlab
patpy

A toolbox for patient or sample representation from single-cell data

666 16 14
genecell
piaso-tools

Precise Integrative Analysis of Single-cell Omics.

648 6 2
genecell
cosg

Accurate and fast cell marker gene identification with COSG

564 59 7
Risitop
transmorph

A unifying data integration framework.

554 11 2
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