Repositories list

• ehrdata

  Public
  A datastructure for EHR data

  data-analysisehrehrapy

  Python

  •

  Apache License 2.0

  •3•5•15•0•Updated Jun 27, 2025Jun 27, 2025

• CellFlow

  Public
  Modeling complex perturbations with CellFlow

  Python

  •

  Other

  •7•58•46•12•Updated Jun 27, 2025Jun 27, 2025

• txsim

  Public
  Python

  •2•3•36•4•Updated Jun 27, 2025Jun 27, 2025

• gh-dashboard

  Public
  A dashboard of everything in the theislab GitHub repository

  HTML

  •0•5•0•0•Updated Jun 27, 2025Jun 27, 2025

• ehrapy

  Public
  Electronic Health Record Analysis with Python.

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

  Python

  •

  Apache License 2.0

  •28•294•42•3•Updated Jun 27, 2025Jun 27, 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 Jun 27, 2025Jun 27, 2025

• ehrapy-datasets

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

  Jupyter Notebook

  •

  Apache License 2.0

  •2•7•2•0•Updated Jun 26, 2025Jun 26, 2025

• FlatVI

  Public
  Jupyter Notebook

  •1•2•0•0•Updated Jun 25, 2025Jun 25, 2025

• CFGen

  Public
  Jupyter Notebook

  •

  MIT License

  •5•17•0•0•Updated Jun 25, 2025Jun 25, 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 Jun 24, 2025Jun 24, 2025

• spatialdata-db

  Public
  Jupyter Notebook

  •

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

  •1•4•26•2•Updated Jun 24, 2025Jun 24, 2025

• cross_system_integration

  Public
  Jupyter Notebook

  •2•13•11•1•Updated Jun 24, 2025Jun 24, 2025

• multigrate

  Public
  Multigrate: multiomic data integration for single-cell genomics

  Python

  •

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

  •7•26•4•2•Updated Jun 23, 2025Jun 23, 2025

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  single-celloptimal-transport

  Python

  •

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

  •10•163•33•5•Updated Jun 23, 2025Jun 23, 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 Jun 23, 2025Jun 23, 2025

• anndata2ri

  Public
  Convert between AnnData and SingleCellExperiment

  jupyterbioconductorsingle-cell+ 2rpy2scanpy

  Python

  •

  GNU General Public License v3.0

  •19•137•14•2•Updated Jun 23, 2025Jun 23, 2025

• devVI

  Public
  Integration of developmental scRNA-seq data

  Python

  •

  MIT License

  •1•0•0•1•Updated Jun 23, 2025Jun 23, 2025

• DRVI

  Public
  Unsupervised Deep Disentangled Representation of Single-Cell Omics

  pythonbioinformaticsintegration+ 4transcriptomicssingle-celldisentanglementanndata

  Python

  •

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

  •3•44•6•2•Updated Jun 23, 2025Jun 23, 2025

• paperbee

  Public
  Python

  •

  MIT License

  •0•14•3•5•Updated Jun 23, 2025Jun 23, 2025

• moscot_notebooks

  Public
  Analysis notebooks using the moscot package

  Jupyter Notebook

  •

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

  •4•8•5•2•Updated Jun 20, 2025Jun 20, 2025

• single-cell-best-practices

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

  tutorialrna-seqbook+ 1single-cell

  Jupyter Notebook

  •

  Other

  •219•934•71•2•Updated Jun 19, 2025Jun 19, 2025

• zellkonverter

  Public
  Conversion between scRNA-seq objects

  rconversionscrna-seq+ 1bioconductor

  R

  •

  Other

  •30•176•12•1•Updated Jun 19, 2025Jun 19, 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 Jun 18, 2025Jun 18, 2025

• regvelo

  Public
  inferring regulatory cellular dynamics

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

  Python

  •

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

  •3•48•3•0•Updated Jun 16, 2025Jun 16, 2025

• hadge

  Public
  Comprehensive pipeline for donor demultiplexing in single cell

  single-celldeconvolutiondemultiplexing

  Nextflow

  •

  MIT License

  •8•24•11•2•Updated Jun 15, 2025Jun 15, 2025

• archmap

  Public
  JavaScript

  •

  MIT License

  •0•4•3•0•Updated Jun 11, 2025Jun 11, 2025

• idtrack

  Public
  Cross-Temporal and Cross-Database Biological Identifier Mapping

  Python

  •

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

  •0•1•1•0•Updated Jun 8, 2025Jun 8, 2025

• archmap_data

  Public
  Python

  •0•1•1•1•Updated Jun 6, 2025Jun 6, 2025

• scProtVelo

  Public
  Jupyter Notebook

  •

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

  •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

• regvelo_reproducibility

  Public
  Jupyter Notebook

  •

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

  •0•8•0•1•Updated Jun 2, 2025Jun 2, 2025