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Single Cell Python Packages

Python packages with the GitHub topic single-cell. Sorted by relevance, with stars and monthly downloads.
single-cell-data
tiledbsoma

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

77K 124 30
scverse
decoupler

Python package to perform enrichment analysis from omics data.

50K 268 36
theislab
anndata2ri

Convert between AnnData and SingleCellExperiment

28K 149 19
vitessce
vitessce

Python API and Jupyter widget for Vitessce

24K 66 12
saezlab
liana

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

19K 287 33
Teichlab
celltypist

A tool for semi-automatic cell type classification

16K 478 59
Starlitnightly
omicverse

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

11K 989 126
aertslab
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.

9K 606 211
KrishnaswamyLab
phate

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

8K 547 82
settylab
mellon

Non-parametric density inference for single-cell analysis.

8K 74 4
scverse
pertpy

Single-cell perturbation analysis

6K 311 59
scverse
rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

5K 370 46
Ekin-Kahraman
rustscenic

Rust and PyO3 implementation of SCENIC-style single-cell regulatory-network analysis. GRN, AUCell, topics, cisTarget, peak calling, cell QC, enhancer-gene links, and eRegulon assembly in one pip install.

5K 11 2
lilab-bcb
cirrocumulus

Bring your single-cell data to life

5K 97 17
velocyto-team
velocyto

RNA velocity estimation in Python

4K 176 84
bowang-lab
scgpt

Large-scale generative pretrain of single cell using transformer.

4K 2K 333
lhqing
allcools

Toolkit for single-cell DNA methylation analysis.

4K 48 22
icbi-lab
infercnvpy

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

4K 189 32
cafferychen777
chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

3K 37 9
ilaykav
scvelo-rs

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

3K 12 0
faridrashidi
trisicell

No description available

3K 14 2
theislab
scarches

Reference mapping for single-cell genomics

3K 404 70
ShobiStassen
pyvia

trajectory inference

2K 109 23
scverse
rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

2K 370 46
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