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scverse
scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

77K 2K 447
scverse
muon

muon is a multimodal omics Python framework

28K 266 36
Teichlab
celltypist

A tool for semi-automatic cell type classification

17K 473 60
dpeerlab
palantir

Single cell trajectory detection

6K 309 61
lilab-bcb
cirrocumulus

Bring your single-cell data to life

4K 97 18
pachterlab
kb-python

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

4K 187 29
aristoteleo
dynamo-release

Mapping Vector Field of Single Cells

4K 490 60
JonathanShor
doubletdetection

Doublet detection in single-cell RNA-seq data.

3K 98 22
theislab
scarches

Reference mapping for single-cell genomics

3K 404 70
broadinstitute
tangram-sc

Spatial alignment of single cell transcriptomic data.

3K 362 64
YosefLab
scvi

Deep probabilistic analysis of single-cell and spatial omics data

2K 2K 447
chanzuckerberg
cellxgene

An interactive explorer for single-cell transcriptomics data

2K 766 150
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
cbg-ethz
scdef

Deep exponential families for single-cell data.

2K 20 1
eleozzr
desc

Deep Embedding for Single-cell Clustering

2K 89 25
quadbio
cellmapper

k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.

1K 13 4
Novartis
cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

1K 68 41
bodegalab
irescue

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

988 22 3
scDiffEq
larry-dataset

Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning

887 4 1
theislab
scgen

Single cell perturbation prediction

866 342 69
potulabe
symphonypy

Port of symphony algorithm of single-cell reference atlas mapping to Python

802 33 3
mtvector
antipode

Variational Inference for Cell Type Evolution

710 6 0
stefanpeidli
mousipy

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

690 30 5
klarman-cell-observatory
scplot

Single cell interactive plotting tools

688 24 8
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