Repositories list

• scib

  Public
  Benchmarking analysis of data integration tools

  Python

  •

  MIT License

  •7676 forks•411411 stars•3838 issues•66 pull requests•Updated Apr 24, 2026Apr 24, 2026

• gh-dashboard

  Public
  A dashboard of everything in the theislab GitHub repository

  HTML

  •00 forks•88 stars•11 issue•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• ehrapy

  Public
  Electronic Health Record Analysis with Python.

  ehrelectronic-health-recordscverse+ 1

  ehrelectronic-health-recordscverseelectronic-medical-record

  Python

  •

  Apache License 2.0

  •4545 forks•345345 stars•2020 issues•44 pull requests•Updated Apr 24, 2026Apr 24, 2026

• ehrdata

  Public
  A datastructure for EHR data

  data-analysisehrehrapy

  data-analysisehrehrapy

  Python

  •

  Apache License 2.0

  •66 forks•1010 stars•77 issues•11 pull request•Updated Apr 23, 2026Apr 23, 2026

• DRVI

  Public
  Unsupervised Deep Disentangled Representation of Single-Cell Omics

  pythonbioinformaticsintegration+ 4

  pythonbioinformaticsintegrationtranscriptomicssingle-celldisentanglementanndata

  Python

  •

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

  •55 forks•6363 stars•44 issues•22 pull requests•Updated Apr 23, 2026Apr 23, 2026

• anndata2ri

  Public
  Convert between AnnData and SingleCellExperiment

  jupyterbioconductorsingle-cell+ 2

  jupyterbioconductorsingle-cellrpy2scanpy

  Python

  •

  GNU General Public License v3.0

  •1919 forks•149149 stars•1313 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• scConcept

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

  Python

  •

  MIT License

  •44 forks•2525 stars•11 issue•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• archmap_data

  Public
  Python

  •00 forks•11 star•11 issue•11 pull request•Updated Apr 21, 2026Apr 21, 2026

• scRatio

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•44 stars•00 issues•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• scanpydoc

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

  Python

  •

  GNU General Public License v3.0

  •55 forks•1212 stars•44 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• troutpy

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

  Jupyter Notebook

  •

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

  •22 forks•2828 stars•00 issues•22 pull requests•Updated Apr 20, 2026Apr 20, 2026

• spatialdata-db

  Public
  Jupyter Notebook

  •

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

  •11 fork•1010 stars•2626 issues•33 pull requests•Updated Apr 20, 2026Apr 20, 2026

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  single-celloptimal-transport

  single-celloptimal-transport

  Python

  •

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

  •1616 forks•205205 stars•3131 issues•55 pull requests•Updated Apr 20, 2026Apr 20, 2026

• multigrate

  Public
  Multigrate: multiomic data integration for single-cell genomics

  Python

  •

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

  •88 forks•3232 stars•66 issues•22 pull requests•Updated Apr 20, 2026Apr 20, 2026

• mapqc

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

  integrationmappingtranscriptomics+ 3

  integrationmappingtranscriptomicssingle-cellatlasquery-to-reference-mapping

  Python

  •

  MIT License

  •11 fork•1111 stars•00 issues•22 pull requests•Updated Apr 20, 2026Apr 20, 2026

• CellFlow

  Public
  Modeling complex perturbations with CellFlow

  Python

  •

  MIT License

  •2525 forks•137137 stars•5050 issues•1616 pull requests•Updated Apr 20, 2026Apr 20, 2026

• single-cell-best-practices

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

  tutorialrna-seqbook+ 1

  tutorialrna-seqbooksingle-cell

  Jupyter Notebook

  •

  Other

  •267267 forks•1.2k1.2k stars•7272 issues•33 pull requests•Updated Apr 20, 2026Apr 20, 2026

• lamin_dataloader

  Public
  Python

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• CellFlow2

  Public
  Modeling complex perturbations with CellFlow

  Python

  •

  Other

  •22 forks•99 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• zellkonverter

  Public
  Conversion between scRNA-seq objects

  rconversionbioconductor+ 1

  rconversionbioconductorscrna-seq

  R

  •

  Other

  •3232 forks•206206 stars•1414 issues•22 pull requests•Updated Apr 16, 2026Apr 16, 2026

• destiny

  Public
  R package for single cell and other data analysis using diffusion maps

  rdimensionality-reductiondiffusion-maps

  rdimensionality-reductiondiffusion-maps

  R

  •

  GNU General Public License v3.0

  •1313 forks•9797 stars•3131 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• cellink

  Public
  Scalable framework for integrating single-cell omics with genetic data using AnnData.

  geneticssingle-cellanndata

  geneticssingle-cellanndata

  Python

  •

  Apache License 2.0

  •44 forks•1414 stars•88 issues•44 pull requests•Updated Apr 14, 2026Apr 14, 2026

• ehrapy-tutorials

  Public
  Tutorials for ehrapy

  Jupyter Notebook

  •

  Apache License 2.0

  •22 forks•99 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• comparative_atlas

  Public
  Incremental Atlas Expansion with case-control scRNAseq data

  Python

  •

  Apache License 2.0

  •00 forks•55 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• jump-cpg0016-segmentation

  Public
  Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium

  Jupyter Notebook

  •

  MIT License

  •00 forks•99 stars•11 issue•11 pull request•Updated Apr 11, 2026Apr 11, 2026

• sctram

  Public
  Single Cell Trajectory Representation Metrics

  Jupyter Notebook

  •

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

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• perturbation-metrics

  Public
  Jupyter Notebook

  •

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

  •00 forks•99 stars•00 issues•11 pull request•Updated Apr 9, 2026Apr 9, 2026

• archmap_doc

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• geome

  Public
  microscopygraph-learningpytorch-geometric+ 1

  microscopygraph-learningpytorch-geometricanndata

  Python

  •

  MIT License

  •44 forks•1515 stars•77 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• archmap

  Public
  JavaScript

  •

  MIT License

  •00 forks•44 stars•44 issues•00 pull requests•Updated Apr 4, 2026Apr 4, 2026