Repositories list

• champollion

  Public
  A novel method for bridge integration (i.e. integration of partially paired single-cell multimodal data): Champollion

  Python

  •

  GNU General Public License v3.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 25, 2026Apr 25, 2026

• champollion_reproducibility

  Public
  Repository to reproduce experiments in "CHAMPOLLION: Robust Multi-Omics Integration via Inverse Optimal Transport Using Paired Cells".

  Jupyter Notebook

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

• recon_reproducibility

  Public
  RECON paper reproducibility repository

  Jupyter Notebook

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

• scPRINT-2

  Public
  🏃🏃 Your next-gen single-cell Foundation Model

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •33 forks•2929 stars•33 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• Circe

  Public
  Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.

  gene-regulationatac-seqgraphical-lasso+ 2

  gene-regulationatac-seqgraphical-lassosingle-cell-atac-seqcis-regulatory-elements

  Python

  •

  Other

  •22 forks•3434 stars•11 issue•11 pull request•Updated Mar 26, 2026Mar 26, 2026

• ReCoN

  Public
  Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations

  single-celltreatment-effectsbiological-networks+ 1

  single-celltreatment-effectsbiological-networksmulticellular

  Python

  •

  GNU General Public License v3.0

  •00 forks•88 stars•00 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• CellOracle

  Public
  This is a lite version of the CellOracle package to run functions necessary to HuMMuS and ReCoN while increasing dependencies flexibility

  Python

  •

  Other

  •7474 forks•11 star•00 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• Xpressor

  Public
  fork of scPRINT for the Xpressor and ESM2-finetuning ICML paper

  Jupyter Notebook

  •

  MIT License

  •00 forks•44 stars•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• DynamicNetworkExplorer

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 18, 2026Mar 18, 2026

• scPRINT

  Public
  🏃 The go-to single-cell Foundation Model

  open-sourceaiembeddings+ 15

  open-sourceaiembeddingsrnaseqsprintzero-shot-learningdenoisingsingle-cell-rna-seqcell-biologybatch-correction+ 8

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2323 forks•146146 stars•00 issues•00 pull requests•Updated Feb 20, 2026Feb 20, 2026

• GRnnData

  Public
  Awesome GRN enhanced AnnData toolkit

  rna-sequtilssingle-cell+ 3

  rna-sequtilssingle-cellgene-regulatory-networkanndatascverse

  Jupyter Notebook

  •

  MIT License

  •22 forks•1111 stars•00 issues•11 pull request•Updated Feb 19, 2026Feb 19, 2026

• .github

  Public
  home page

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

• CIRCE_reproducibility

  Public
  Reproducibility code of the Circe (Trimbour et al., 2025) publication

  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jan 18, 2026Jan 18, 2026

• HuMMuS

  Public
  Molecular interactions inference from single-cell multi-omics data

  transcriptomicssingle-cellbiological-networks+ 3

  transcriptomicssingle-cellbiological-networksepigenomicsmultilayer-networksmulti-omics

  R

  •

  GNU Affero General Public License v3.0

  •77 forks•3131 stars•77 issues•22 pull requests•Updated Jan 14, 2026Jan 14, 2026

• scconfluence

  Public
  A novel method for single-cell diagonal integration: scConfluence

  integrationsingle-celldimension-reduction+ 2

  integrationsingle-celldimension-reductionoptimal-transportmultiomics

  Python

  •

  GNU General Public License v3.0

  •11 fork•2727 stars•22 issues•00 pull requests•Updated Nov 3, 2025Nov 3, 2025

• stories

  Public
  Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein

  Python

  •

  GNU General Public License v3.0

  •55 forks•2727 stars•11 issue•00 pull requests•Updated Oct 21, 2025Oct 21, 2025

• celloracle_recon

  Public
  Lite version of CellOracle (Morris-Lab) to make it compatible with ReCoN and HuMMuS

  00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2025Sep 22, 2025

• Mowgli

  Public
  Single-cell multi-omics integration using Optimal Transport

  matrix-factorizationsingle-celldictionary-learning+ 3

  matrix-factorizationsingle-celldictionary-learningoptimal-transportmulti-omicsmulti-omics-integration

  Python

  •

  GNU General Public License v3.0

  •55 forks•5151 stars•00 issues•00 pull requests•Updated Aug 14, 2025Aug 14, 2025

• benGRN

  Public
  Awesome Benchmark of Gene Regulatory Networks

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 27, 2025Jan 27, 2025

• scPRINT-old1

  Public archive
  Single Cell Pretrained Regulatory network INference from Transcripts

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•1111 stars•00 issues•00 pull requests•Updated Sep 17, 2024Sep 17, 2024

• scDataLoader

  Public
  a dataloader to work with large single cell datasets from lamindb

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •66 forks•00 stars•00 issues•00 pull requests•Updated Sep 16, 2024Sep 16, 2024

• stories_reproducibility

  Public
  STORIES: Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein

  Jupyter Notebook

  •22 forks•44 stars•00 issues•00 pull requests•Updated Jul 9, 2024Jul 9, 2024

• mowgli_reproducibility

  Public
  Data and scripts to reproduce experiments for Mowgli.

  matrix-factorizationreproducibilitysingle-cell+ 3

  matrix-factorizationreproducibilitysingle-celldictionary-learningoptimal-transportmulti-omics

  Python

  •11 fork•66 stars•11 issue•00 pull requests•Updated Apr 1, 2024Apr 1, 2024

• scc_reproducibility

  Public
  Jupyter Notebook

  •00 forks•44 stars•11 issue•00 pull requests•Updated Feb 29, 2024Feb 29, 2024

• momix-notebook

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1414 forks•6666 stars•33 issues•11 pull request•Updated Nov 14, 2023Nov 14, 2023

• OT-scOmics

  Public
  This Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in between single-cell om…

  biologygpusingle-cell+ 1

  biologygpusingle-celloptimal-transport

  Python

  •

  GNU General Public License v3.0

  •88 forks•4343 stars•00 issues•00 pull requests•Updated Feb 3, 2023Feb 3, 2023

• scNET

  Public
  jupyther notebook comparing reproducibility of single-cell network inference algorithms

  Jupyter Notebook

  •22 forks•44 stars•22 issues•11 pull request•Updated Sep 15, 2021Sep 15, 2021