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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.

49K 267 36
saezlab
liana

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

28K 283 32
vitessce
vitessce

Python API and Jupyter widget for Vitessce

25K 66 12
theislab
anndata2ri

Convert between AnnData and SingleCellExperiment

25K 149 19
Teichlab
celltypist

A tool for semi-automatic cell type classification

17K 473 60
Starlitnightly
omicverse

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

14K 972 126
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.

10K 600 210
settylab
mellon

Non-parametric density inference for single-cell analysis.

9K 73 4
KrishnaswamyLab
phate

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

9K 546 82
scverse
pertpy

Single-cell perturbation analysis

7K 309 56
scverse
rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

7K 360 43
velocyto-team
velocyto

RNA velocity estimation in Python

4K 175 84
bowang-lab
scgpt

Large-scale generative pretrain of single cell using transformer.

4K 2K 334
lilab-bcb
cirrocumulus

Bring your single-cell data to life

4K 97 18
ShobiStassen
pyvia

trajectory inference

4K 108 21
lhqing
allcools

Toolkit for single-cell DNA methylation analysis.

3K 47 22
icbi-lab
infercnvpy

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

3K 189 32
theislab
scarches

Reference mapping for single-cell genomics

3K 404 70
faridrashidi
trisicell

No description available

3K 14 2
aertslab
scatac-fragment-tools

Tools for working with scATAC-seq fragment files

2K 7 1
faridrashidi
scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

2K 7 1
becavin-lab
checkatlas

One liner tool to check the quality of your single-cell atlases.

2K 3 2
theislab
moscot

Multi-omic single-cell optimal transport tools

2K 206 16
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