Repositories list

• gh-dashboard

  Public
  A dashboard of everything in the theislab GitHub repository

  HTML

  •0•6•1•0•Updated Aug 28, 2025Aug 28, 2025

• regvelo

  Public
  inferring regulatory cellular dynamics

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

  Python

  •

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

  •6•54•2•0•Updated Aug 28, 2025Aug 28, 2025

• CellFlow

  Public
  Modeling complex perturbations with CellFlow

  Python

  •

  Other

  •11•83•48•13•Updated Aug 27, 2025Aug 27, 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 27, 2025Aug 27, 2025

• prophet

  Public
  Jupyter Notebook

  •

  MIT License

  •2•36•3•0•Updated Aug 27, 2025Aug 27, 2025

• ehrapy

  Public
  Electronic Health Record Analysis with Python.

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

  Python

  •

  Apache License 2.0

  •35•303•41•3•Updated Aug 26, 2025Aug 26, 2025

• scanpydoc

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

  Python

  •

  GNU General Public License v3.0

  •6•12•2•0•Updated Aug 26, 2025Aug 26, 2025

• anndata2ri

  Public
  Convert between AnnData and SingleCellExperiment

  jupyterbioconductorsingle-cell+ 2rpy2scanpy

  Python

  •

  GNU General Public License v3.0

  •19•138•13•0•Updated Aug 26, 2025Aug 26, 2025

• zellkonverter

  Public
  Conversion between scRNA-seq objects

  rconversionscrna-seq+ 1bioconductor

  R

  •

  Other

  •31•183•10•1•Updated Aug 26, 2025Aug 26, 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 25, 2025Aug 25, 2025

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  single-celloptimal-transport

  Python

  •

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

  •11•171•30•5•Updated Aug 25, 2025Aug 25, 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 25, 2025Aug 25, 2025

• spatialdata-db

  Public
  Jupyter Notebook

  •

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

  •1•5•26•3•Updated Aug 25, 2025Aug 25, 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 25, 2025Aug 25, 2025

• ehrdata

  Public
  A datastructure for EHR data

  data-analysisehrehrapy

  Python

  •

  Apache License 2.0

  •3•7•16•1•Updated Aug 25, 2025Aug 25, 2025

• devVI

  Public
  Integration of developmental scRNA-seq data

  Python

  •

  MIT License

  •1•0•0•1•Updated Aug 25, 2025Aug 25, 2025

• DRVI

  Public
  Unsupervised Deep Disentangled Representation of Single-Cell Omics

  pythonbioinformaticsintegration+ 4transcriptomicssingle-celldisentanglementanndata

  Python

  •

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

  •3•48•6•2•Updated Aug 25, 2025Aug 25, 2025

• quicat

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

• regvelo_reproducibility

  Public
  Jupyter Notebook

  •

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

  •0•8•0•0•Updated Aug 20, 2025Aug 20, 2025

• paperbee

  Public
  Python

  •

  MIT License

  •9•66•6•5•Updated Aug 20, 2025Aug 20, 2025

• ehrapy-datasets

  Public
  A collection of scripts to generate AnnData objects of EHR datasets for ehrapy

  Jupyter Notebook

  •

  Apache License 2.0

  •2•6•4•0•Updated Aug 19, 2025Aug 19, 2025

• quicat_reproducibility

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• hadge

  Public
  Comprehensive pipeline for donor demultiplexing in single cell

  single-celldeconvolutiondemultiplexing

  Nextflow

  •

  MIT License

  •8•24•14•2•Updated Aug 13, 2025Aug 13, 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 Aug 13, 2025Aug 13, 2025

• archmap_data

  Public
  Python

  •0•1•1•1•Updated Aug 12, 2025Aug 12, 2025

• perturbation-metrics

  Public
  Jupyter Notebook

  •

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

  •0•5•0•1•Updated Aug 10, 2025Aug 10, 2025

• FlatVI

  Public
  Jupyter Notebook

  •1•4•1•0•Updated Aug 10, 2025Aug 10, 2025

• pertpy-reproducibility

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •2•3•0•0•Updated Aug 8, 2025Aug 8, 2025

• geome

  Public
  microscopygraph-learningpytorch-geometric+ 1anndata

  Python

  •

  MIT License

  •4•15•7•2•Updated Aug 6, 2025Aug 6, 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