Repositories list

• CellFlow

  Public
  Modeling complex perturbations with CellFlow

  Python

  •

  Other

  •10•74•47•13•Updated Aug 5, 2025Aug 5, 2025

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  single-celloptimal-transport

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •10•168•29•5•Updated Aug 4, 2025Aug 4, 2025

• troutpy

  Public
  Package for the analysis of Transcripts outside segmented cells in ST data

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•1•Updated Aug 4, 2025Aug 4, 2025

• multigrate

  Public
  Multigrate: multiomic data integration for single-cell genomics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •8•27•4•3•Updated Aug 4, 2025Aug 4, 2025

• spatialdata-db

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•5•26•3•Updated Aug 4, 2025Aug 4, 2025

• mapqc

  Public
  MapQC - a metric for the evaluation of single-cell query-to-reference mappings

  integrationmappingtranscriptomics+ 3single-cellatlasquery-to-reference-mapping

  Python

  •

  MIT License

  •1•9•0•1•Updated Aug 4, 2025Aug 4, 2025

• DRVI

  Public
  Unsupervised Deep Disentangled Representation of Single-Cell Omics

  pythonbioinformaticsintegration+ 4transcriptomicssingle-celldisentanglementanndata

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•46•5•2•Updated Aug 4, 2025Aug 4, 2025

• scanpydoc

  Public
  Collection of Sphinx extensions similar to (but more flexible than) numpydoc

  Python

  •

  GNU General Public License v3.0

  •6•12•2•1•Updated Aug 4, 2025Aug 4, 2025

• ehrdata

  Public
  A datastructure for EHR data

  data-analysisehrehrapy

  Python

  •

  Apache License 2.0

  •3•7•16•1•Updated Aug 4, 2025Aug 4, 2025

• ehrapy

  Public
  Electronic Health Record Analysis with Python.

  ehrelectronic-health-recordscverse+ 1electronic-medical-record

  Python

  •

  Apache License 2.0

  •31•298•41•4•Updated Aug 4, 2025Aug 4, 2025

• anndata2ri

  Public
  Convert between AnnData and SingleCellExperiment

  jupyterbioconductorsingle-cell+ 2rpy2scanpy

  Python

  •

  GNU General Public License v3.0

  •19•137•14•2•Updated Aug 4, 2025Aug 4, 2025

• devVI

  Public
  Integration of developmental scRNA-seq data

  Python

  •

  MIT License

  •1•0•0•1•Updated Aug 4, 2025Aug 4, 2025

• hadge

  Public
  Comprehensive pipeline for donor demultiplexing in single cell

  single-celldeconvolutiondemultiplexing

  Nextflow

  •

  MIT License

  •8•24•11•1•Updated Aug 4, 2025Aug 4, 2025

• gh-dashboard

  Public
  A dashboard of everything in the theislab GitHub repository

  HTML

  •0•5•2•0•Updated Aug 4, 2025Aug 4, 2025

• spatial_scooby

  Public
  spatial_scooby: Modeling spatial transcriptomics from DNA sequence at single-cell resolution.

  Python

  •

  MIT License

  •4•0•0•0•Updated Aug 4, 2025Aug 4, 2025

• regvelo

  Public
  inferring regulatory cellular dynamics

  generative-modelrna-velocity-estimationperturbation-analysis+ 2grn-inferencesingle-cell-dynamics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •4•50•1•0•Updated Aug 2, 2025Aug 2, 2025

• cellrank_protocol

  Public
  Repository accompanying CellRank's Nature Protocols article.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

• cellflow_reproducibility

  Public
  Reproducibility repository for CellFlow

  Jupyter Notebook

  •2•2•0•0•Updated Jul 28, 2025Jul 28, 2025

• tissue

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Jul 26, 2025Jul 26, 2025

• multimil_reproducibility

  Public
  Jupyter Notebook

  •1•6•4•0•Updated Jul 24, 2025Jul 24, 2025

• pertpy-reproducibility

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •2•3•0•0•Updated Jul 24, 2025Jul 24, 2025

• archmap_data

  Public
  Python

  •0•1•1•1•Updated Jul 23, 2025Jul 23, 2025

• scarches

  Public
  Reference mapping for single-cell genomics

  deep-learningscrna-seqdata-integration+ 7single-cellrna-seq-analysissingle-cell-genomicsbatch-correctionmultimodal-deep-learningmultiomicshuman-cell-atlas

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •63•375•53•9•Updated Jul 23, 2025Jul 23, 2025

• paperbee

  Public
  Python

  •

  MIT License

  •7•60•5•8•Updated Jul 21, 2025Jul 21, 2025

• archmap_doc

  Public
  Python

  •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

• deconvATAC

  Public
  Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•5•0•0•Updated Jul 17, 2025Jul 17, 2025

• sample-prediction-pipeline

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Jul 17, 2025Jul 17, 2025

• single-cell-best-practices

  Public
  https://www.sc-best-practices.org

  tutorialrna-seqbook+ 1single-cell

  Jupyter Notebook

  •

  Other

  •226•977•72•2•Updated Jul 17, 2025Jul 17, 2025

• spatial_pancreas

  Public
  Spatial human pancreas atlas in the context of T1D (Colab with Sander Lab and Gaulton)

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

• multimil

  Public
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•33•9•1•Updated Jul 14, 2025Jul 14, 2025