Repositories list

• CellFlow2

  Public
  Modeling complex perturbations with CellFlow

  Python

  •

  Other

  •16•1•0•0•Updated Oct 19, 2025Oct 19, 2025

• gh-dashboard

  Public
  A dashboard of everything in the theislab GitHub repository

  HTML

  •0•7•1•0•Updated Oct 19, 2025Oct 19, 2025

• hadge

  Public
  Comprehensive pipeline for donor demultiplexing in single cell

  single-celldeconvolutiondemultiplexing

  Nextflow

  •

  MIT License

  •8•24•14•1•Updated Oct 19, 2025Oct 19, 2025

• ehrapy

  Public
  Electronic Health Record Analysis with Python.

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

  Python

  •

  Apache License 2.0

  •36•308•33•1•Updated Oct 17, 2025Oct 17, 2025

• DRVI

  Public
  Unsupervised Deep Disentangled Representation of Single-Cell Omics

  pythonbioinformaticsintegration+ 4transcriptomicssingle-celldisentanglementanndata

  Python

  •

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

  •5•53•6•2•Updated Oct 17, 2025Oct 17, 2025

• archmap_data

  Public
  Python

  •0•1•1•1•Updated Oct 17, 2025Oct 17, 2025

• ehrdata

  Public
  A datastructure for EHR data

  data-analysisehrehrapy

  Python

  •

  Apache License 2.0

  •4•8•21•2•Updated Oct 16, 2025Oct 16, 2025

• scConcept

  Public
  Contrastive pre-training for technology-agnostic single-cell representations beyond reconstruction

  Python

  •0•3•0•0•Updated Oct 15, 2025Oct 15, 2025

• scaling_flow

  Public
  CellFlow across datasets, à la Prophet

  Python

  •

  Other

  •16•2•0•0•Updated Oct 14, 2025Oct 14, 2025

• cellflow_reproducibility

  Public
  Reproducibility repository for CellFlow

  Jupyter Notebook

  •3•2•0•1•Updated Oct 14, 2025Oct 14, 2025

• anndata2ri

  Public
  Convert between AnnData and SingleCellExperiment

  jupyterbioconductorsingle-cell+ 2rpy2scanpy

  Python

  •

  GNU General Public License v3.0

  •19•142•13•0•Updated Oct 14, 2025Oct 14, 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 Oct 13, 2025Oct 13, 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•2•Updated Oct 13, 2025Oct 13, 2025

• troutpy

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

  Jupyter Notebook

  •

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

  •1•7•0•2•Updated Oct 13, 2025Oct 13, 2025

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  single-celloptimal-transport

  Python

  •

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

  •12•175•30•5•Updated Oct 13, 2025Oct 13, 2025

• multigrate

  Public
  Multigrate: multiomic data integration for single-cell genomics

  Python

  •

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

  •8•27•4•3•Updated Oct 13, 2025Oct 13, 2025

• devVI

  Public
  Integration of developmental scRNA-seq data

  Python

  •

  MIT License

  •1•0•0•2•Updated Oct 13, 2025Oct 13, 2025

• spatialdata-db

  Public
  Jupyter Notebook

  •

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

  •1•5•26•3•Updated Oct 13, 2025Oct 13, 2025

• CellFlow

  Public
  Modeling complex perturbations with CellFlow

  Python

  •

  Other

  •16•89•49•16•Updated Oct 13, 2025Oct 13, 2025

• spatialdata-db-curation

  Public
  Structure to manage and formalise data submission for SpatialData-DB

  Python

  •0•0•0•0•Updated Oct 6, 2025Oct 6, 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

  •64•384•55•9•Updated Oct 2, 2025Oct 2, 2025

• regvelo_reproducibility

  Public
  Jupyter Notebook

  •

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

  •0•8•0•0•Updated Oct 1, 2025Oct 1, 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•35•10•1•Updated Sep 30, 2025Sep 30, 2025

• scproto

  Public
  Interpretable self-supervised prototype learning for denoising and integrating single-cell transcriptomic data via biologically meaningful metacells.

  Jupyter Notebook

  •1•4•0•0•Updated Sep 30, 2025Sep 30, 2025

• spapros

  Public
  Python package for Probe set selection for targeted spatial transcriptomics.

  Python

  •

  MIT License

  •8•44•8•9•Updated Sep 29, 2025Sep 29, 2025

• prophet-reproducibility

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 28, 2025Sep 28, 2025

• prophet

  Public
  Jupyter Notebook

  •

  MIT License

  •2•35•4•0•Updated Sep 26, 2025Sep 26, 2025

• regvelo

  Public
  inferring regulatory cellular dynamics

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

  Python

  •

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

  •5•58•2•0•Updated Sep 24, 2025Sep 24, 2025

• rapids_singlecell-reproducibility

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• DRVI_reproducibility

  Public
  Reproducibility repository of DRVI

  Jupyter Notebook

  •1•3•0•0•Updated Sep 23, 2025Sep 23, 2025