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Plate V

Software

Panorama of 36 software tools by GitHub stars
Namestars
Scanpy2609
single-cell-tutorial1599
Single-cell best practices1299
anndata783
scVelo515
scib436
scArches414
ehrapy370
scGen361
single-cell-transformer-papers343
dca275
paga249
moscot219
zellkonverter209
scCODA205
regvelo200
sc-pert186
kBET181
nicheformer179
CellFlow166
chemCPA162
CPA157
anndata2ri154
paperbee137
sfaira135
ncem121
destiny114
scib-pipeline85
DRVI83
scib-reproducibility76
scTab70
AutoGeneS64
trVAE63
spatial_scog_workshop_202254
neural_organoid_atlas53
spapros51

Pl. V The tools we build and maintain as an alpine panorama: every tool a summit, its height its GitHub stars on a log scale and its elevation given after its name; the featured tools stand in the front range, the others in the ranges behind. Select a summit to open the tool; below, every tool with its releases, downloads and build status.

36 repositories, 12,377 stars in all, from GitHub, PyPI and conda · data synced 6 Nov 2026

36 tools12.4K starsGitHub organisation

All tools36

Sorted by stars. Release age and CI status as of 6 November 2026; downloads: PyPI in the last month (pypistats), conda in total (anaconda.org).
ToolStarsLatest releaseDownloadsCILanguage
ScanpySingle-cell analysis in Python. Scales to >100M cells.2.6K1.12.58 days ago747.6K PyPI/moPassingPython
single-cell-tutorialSingle cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"1.6KNo release––Jupyter Notebook
Single-cell best practiceshttps://www.sc-best-practices.org1.3K0.2.08 days ago–PassingJupyter Notebook
anndataAnnotated data.7830.13.449 days ago1.3M PyPI/moFailingPython
scVeloRNA velocity generalized through dynamical modeling.515v0.3.48 months ago7.7K PyPI/mo38.4K condaFailingPython
scibBenchmarking analysis of data integration tools.436v1.2.16 months ago8.3K PyPI/mo9K condaPassingPython
scArchesReference mapping for single-cell genomics.414v0.5.13 years ago693 PyPI/mo1.4K conda–Jupyter Notebook
ehrapyElectronic Health Record Analysis with Python.370v0.16.04 days ago572 PyPI/moPassingPython
scGenSingle cell perturbation prediction.361v2.1.05 years ago337 PyPI/mo–Python
single-cell-transformer-papers343No release–PassingHTML
dcaDeep count autoencoder for denoising scRNA-seq data275v0.3.16 years ago115 PyPI/mo48.2K condaFailingPython
pagaMapping out the coarse-grained connectivity structures of complex manifolds.249No release––Jupyter Notebook
moscotMulti-omic single-cell optimal transport tools.219v0.5.22 months ago804 PyPI/mo12.8K condaFailingPython
zellkonverterConversion between scRNA-seq objects209v1.22.06 months ago–FailingR
scCODAA Bayesian model for compositional single-cell data analysis205v0.1.94 years ago828 PyPI/mo1.4K conda–Jupyter Notebook
regveloinferring regulatory cellular dynamics200v0.4.210 months ago200 PyPI/moPassingPython
sc-pertModels and datasets for perturbational single-cell omics186No release––Jupyter Notebook
kBETAn R package to test for batch effects in high-dimensional single-cell RNA sequencing data.181First_minor7 years ago––HTML
nicheformerRepository for Nicheformer: a foundation model for single-cell and spatial omics179No release––Jupyter Notebook
CellFlowModeling complex perturbations with CellFlow166v0.0.97 months ago–FailingPython
chemCPACode for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.162No release––Jupyter Notebook
CPAThe Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level.157v0.5.03 years ago––Python
anndata2riConvert between AnnData and SingleCellExperiment154v2.0.14 months ago1.7K PyPI/mo65.3K condaFailingPython
paperbeeLLM-powered personalized daily lists of scientific papers137v1.2.110 months ago16 PyPI/moPassingPython
sfairadata and model repository for single-cell data135v0.3.133 years ago––Python
ncemLearning cell communication from spatial graphs of cells1210.1.53 years ago42 PyPI/mo–Python
destinyR package for single cell and other data analysis using diffusion maps114No release––R
scib-pipelineSnakemake pipeline that works with the scIB package to benchmark data integration methods.85No release––Python
DRVIUnsupervised Deep Disentangled Representation of Single-Cell Omics83v0.2.823 days ago–PassingPython
scib-reproducibilityAdditional code and analysis from the single-cell integration benchmarking project76No release––Jupyter Notebook
scTab700.12 years ago––Jupyter Notebook
AutoGeneS64No release53 PyPI/mo3.2K conda–Jupyter Notebook
trVAEConditional out-of-distribution prediction63v1.1.26 years ago26 PyPI/mo–Python
spatial_scog_workshop_2022Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 202254No release––Jupyter Notebook
neural_organoid_atlasReproducibility repository for the Human Neural Organoid Atlas publication53No release––Jupyter Notebook
spaprosPython package for Probe set selection for targeted spatial transcriptomics.510.1.612 months ago62 PyPI/mo738 condaFailingPython