Repositories list

• CostaLab_python_integration

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• PILOT

  Public

  CostaLab/PILOT’s past year of commit activity
  Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

  single-celldigital-pathologydisease-progression+ 2

  single-celldigital-pathologydisease-progressionmulti-scale-single-celldisease-trajectory

  Python

  •

  MIT License

  •88 forks•2626 stars•11 issue•11 pull request•Updated Apr 22, 2026Apr 22, 2026

• PILOT-GM-VAE

  Public
  Patient-Level Analysis of Single Cell Disease Atlas with Optimal Transport of Gaussian Mixtures Variational Autoencoders

  single-celloptimal-transportvariational-autoencoder+ 3

  single-celloptimal-transportvariational-autoencoderdisease-progressionguassian-mixture-modelmulti-scale-single-cell

  Python

  •

  Other

  •22 forks•88 stars•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• pyCrossTalkeR

  Public
  pyCrossTalkeR is a framework for network analysis and visualisation of Ligand Receptor networks

  Jupyter Notebook

  •

  MIT License

  •11 fork•33 stars•00 issues•22 pull requests•Updated Apr 22, 2026Apr 22, 2026

• sc2marker

  Public
  Surface Marker Detection Using Single Cell Data

  single-cellmarker-detection

  single-cellmarker-detection

  HTML

  •

  MIT License

  •33 forks•1212 stars•22 issues•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• scrna_seurat_pipeline

  Public
  comprehensive analysis of single-cell transcriptomics data

  R

  •99 forks•2525 stars•44 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• CrossTalkeR

  Public

  CostaLab/CrossTalkeR’s past year of commit activity
  R package to do the Ligand Receptor Analysis Visualization

  networksingle-cellcell-cell-communication

  networksingle-cellcell-cell-communication

  Jupyter Notebook

  •

  MIT License

  •99 forks•4949 stars•33 issues•00 pull requests•Updated Mar 24, 2026Mar 24, 2026

• NicheSphere

  Public
  Python

  •

  MIT License

  •11 fork•33 stars•22 issues•00 pull requests•Updated Mar 20, 2026Mar 20, 2026

• scACCorDiON.su

  Public
  R

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 17, 2025Dec 17, 2025

• example_clust_bm_plots

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 16, 2025Dec 16, 2025

• CimpleG

  Public
  CimpleG, an R package to find (small) CpG signatures.

  rmethylationbiomarker-discovery+ 4

  rmethylationbiomarker-discoverydeconvolutionbiomarkerscell-type-classificationcpg-signature

  R

  •

  GNU General Public License v3.0

  •00 forks•88 stars•00 issues•00 pull requests•Updated Dec 5, 2025Dec 5, 2025

• LR2TF

  Public
  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 13, 2025Nov 13, 2025

• phlower

  Public
  Use hodge decomposition for trajectory analysis

  single-cellsimplicial-complextrajectory-inference+ 2

  single-cellsimplicial-complextrajectory-inferencehodge-laplacianhodge-laplacian-decomposition

  Python

  •

  GNU Affero General Public License v3.0

  •22 forks•2424 stars•55 issues•00 pull requests•Updated Nov 12, 2025Nov 12, 2025

• reg-gen

  Public
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

  bioinformaticsdnase-seqgenomics+ 7

  bioinformaticsdnase-seqgenomicsngsmotifchip-seqatac-seqmotif-analysisfootprintingdifferential-peak-calling

  Python

  •

  Other

  •2929 forks•114114 stars•6666 issues•22 pull requests•Updated Nov 3, 2025Nov 3, 2025

• Resources

  Public
  Resources our lab likes :)

  00 forks•11 star•00 issues•00 pull requests•Updated Oct 7, 2025Oct 7, 2025

• scACCorDiON

  Public
  Comparing Directed Weighted Graphs

  Jupyter Notebook

  •

  MIT License

  •11 fork•44 stars•00 issues•00 pull requests•Updated Sep 19, 2025Sep 19, 2025

• sigurd

  Public
  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 12, 2025Aug 12, 2025

• VT3-ISMB-ECCB

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 17, 2025Jul 17, 2025

• bulk_RNASeq

  Public
  Bulk RNAseq R pipeline

  R

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 13, 2025Jan 13, 2025

• MOJITOO

  Public
  MOJITOO: a fast and universal method for integration of multimodal single cell data

  R

  •11 fork•1111 stars•00 issues•00 pull requests•Updated Oct 23, 2024Oct 23, 2024

• phlower-reproducibility

  Public
  Source code for the reproducibility of the PHLOWER manuscript

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 15, 2024Oct 15, 2024

• scMEGA

  Public
  scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference

  single-cellgrnmultiomics

  single-cellgrnmultiomics

  R

  •

  Other

  •33 forks•4545 stars•1212 issues•00 pull requests•Updated Sep 20, 2024Sep 20, 2024

• kidney_injury_lineage

  Public
  Lineage tracing reveals transient phenotypic adaptation of tubular cells during acute kidney injury

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 10, 2024Feb 10, 2024

• ArchRNA

  Public
  ArchR extension to analyze single cells transcriptome

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 28, 2023Feb 28, 2023

• scopen-reproducibility

  Public
  A repository to include all scripts and codes for reproducibility of scOpen manuscript

  HTML

  •11 fork•77 stars•11 issue•00 pull requests•Updated Feb 16, 2023Feb 16, 2023

• scopen

  Public
  scOpen: single-cell open chromatin analysis via NMF modelling

  Python

  •

  GNU General Public License v3.0

  •33 forks•2828 stars•22 issues•00 pull requests•Updated Feb 4, 2023Feb 4, 2023

• CostaLab_PhD_Thesis_Template

  Public
  This is a Latex template for PhD thesis in Costalab

  TeX

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 26, 2022Aug 26, 2022

• mouse_heart_MI

  Public
  Codes for analysis of mouse heart MI scATAC-seq data

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 7, 2022Jun 7, 2022

• spatial_multiomic_mi

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 13, 2022May 13, 2022

• SOSE2022

  Public
  Material for the spring course sc(RNA+ATAC)

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 6, 2022May 6, 2022