Repositories list

• scACCorDiON.su

  Public
  R

  •

  Other

  •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

• scrna_seurat_pipeline

  Public
  comprehensive analysis of single-cell transcriptomics data

  R

  •9•25•4•0•Updated Dec 17, 2025Dec 17, 2025

• example_clust_bm_plots

  Public
  R

  •1•0•0•0•Updated Dec 16, 2025Dec 16, 2025

• CimpleG

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

  rmethylationbiomarker-discovery+ 4deconvolutionbiomarkerscell-type-classificationcpg-signature

  R

  •

  GNU General Public License v3.0

  •0•6•0•0•Updated Dec 5, 2025Dec 5, 2025

• CrossTalkeR

  Public
  R package to do the Ligand Receptor Analysis Visualization

  networksingle-cellcell-cell-communication

  Jupyter Notebook

  •

  MIT License

  •9•48•3•0•Updated Nov 27, 2025Nov 27, 2025

• LR2TF

  Public
  R

  •0•0•0•0•Updated Nov 13, 2025Nov 13, 2025

• phlower

  Public
  Use hodge decomposition for trajectory analysis

  single-cellsimplicial-complextrajectory-inference+ 2hodge-laplacianhodge-laplacian-decomposition

  Python

  •

  GNU Affero General Public License v3.0

  •0•22•3•0•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+ 7ngsmotifchip-seqatac-seqmotif-analysisfootprintingdifferential-peak-calling

  Python

  •

  Other

  •28•111•66•2•Updated Nov 3, 2025Nov 3, 2025

• pyCrossTalkeR

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

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Oct 17, 2025Oct 17, 2025

• Resources

  Public
  Resources our lab likes :)

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

• PILOT

  Public
  Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

  single-celldigital-pathologydisease-progression+ 2multi-scale-single-celldisease-trajectory

  Python

  •

  MIT License

  •6•24•2•1•Updated Oct 6, 2025Oct 6, 2025

• scACCorDiON

  Public
  Comparing Directed Weighted Graphs

  Jupyter Notebook

  •

  MIT License

  •1•4•0•0•Updated Sep 19, 2025Sep 19, 2025

• Nichesphere

  Public
  Jupyter Notebook

  •0•3•0•0•Updated Sep 13, 2025Sep 13, 2025

• sigurd

  Public
  R

  •0•1•0•0•Updated Aug 12, 2025Aug 12, 2025

• VT3-ISMB-ECCB

  Public
  HTML

  •0•0•0•0•Updated Jul 17, 2025Jul 17, 2025

• PILOT-GM-VAE

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

  single-celloptimal-transportvariational-autoencoder+ 3disease-progressionguassian-mixture-modelmulti-scale-single-cell

  Python

  •

  Other

  •1•7•0•0•Updated Jun 13, 2025Jun 13, 2025

• bulk_RNASeq

  Public
  Bulk RNAseq R pipeline

  R

  •

  Other

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• MOJITOO

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

  R

  •1•11•0•0•Updated Oct 23, 2024Oct 23, 2024

• phlower-reproducibility

  Public
  Source code for the reproducibility of the PHLOWER manuscript

  R

  •0•1•0•0•Updated Oct 15, 2024Oct 15, 2024

• scMEGA

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

  single-cellgrnmultiomics

  R

  •

  Other

  •3•43•11•0•Updated Sep 20, 2024Sep 20, 2024

• kidney_injury_lineage

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

  R

  •0•0•0•0•Updated Feb 10, 2024Feb 10, 2024

• ArchRNA

  Public
  ArchR extension to analyze single cells transcriptome

  Jupyter Notebook

  •0•0•0•0•Updated Feb 28, 2023Feb 28, 2023

• scopen-reproducibility

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

  HTML

  •1•7•1•0•Updated Feb 16, 2023Feb 16, 2023

• scopen

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

  Python

  •

  GNU General Public License v3.0

  •3•28•2•0•Updated Feb 4, 2023Feb 4, 2023

• CostaLab_PhD_Thesis_Template

  Public
  This is a Latex template for PhD thesis in Costalab

  TeX

  •

  MIT License

  •0•0•0•0•Updated Aug 26, 2022Aug 26, 2022

• mouse_heart_MI

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

  R

  •

  MIT License

  •0•0•0•0•Updated Jun 7, 2022Jun 7, 2022

• spatial_multiomic_mi

  Public
  HTML

  •0•0•0•0•Updated May 13, 2022May 13, 2022

• SOSE2022

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

  MIT License

  •0•0•0•0•Updated May 6, 2022May 6, 2022

• sc2marker

  Public
  Surface Marker Detection Using Single Cell Data

  single-cellmarker-detection

  HTML

  •

  MIT License

  •2•9•2•0•Updated May 6, 2022May 6, 2022

• costalab.github.io

  Public
  The repository for CostaLab website

  HTML

  •

  MIT License

  •0•0•0•0•Updated Apr 27, 2022Apr 27, 2022