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  1. reg-gen reg-gen Public

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

    Python 111 29

  2. CrossTalkeR CrossTalkeR Public

    R package to do the Ligand Receptor Analysis Visualization

    Jupyter Notebook 49 9

  3. scopen scopen Public

    scOpen: single-cell open chromatin analysis via NMF modelling

    Python 27 3

  4. MOJITOO MOJITOO Public

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

    R 11 1

  5. sc2marker sc2marker Public

    Surface Marker Detection Using Single Cell Data

    HTML 11 2

  6. CimpleG CimpleG Public

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

    R 7

Repositories

Showing 10 of 46 repositories
  • pyCrossTalkeR Public

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

    CostaLab/pyCrossTalkeR’s past year of commit activity
    Jupyter Notebook 2 MIT 0 0 1 Updated Feb 26, 2026
  • NicheSphere Public
    CostaLab/NicheSphere’s past year of commit activity
    Python 3 MIT 1 0 0 Updated Feb 24, 2026
  • scrna_seurat_pipeline Public

    comprehensive analysis of single-cell transcriptomics data

    CostaLab/scrna_seurat_pipeline’s past year of commit activity
    R 25 9 4 0 Updated Feb 21, 2026
  • CrossTalkeR Public

    R package to do the Ligand Receptor Analysis Visualization

    CostaLab/CrossTalkeR’s past year of commit activity
    Jupyter Notebook 49 MIT 9 3 0 Updated Feb 13, 2026
  • PILOT Public

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

    CostaLab/PILOT’s past year of commit activity
    Python 25 MIT 6 3 1 Updated Feb 12, 2026
  • PILOT-GM-VAE Public

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

    CostaLab/PILOT-GM-VAE’s past year of commit activity
    Python 8 1 0 0 Updated Jan 22, 2026
  • CostaLab/scACCorDiON.su’s past year of commit activity
    R 0 0 0 0 Updated Dec 17, 2025
  • CostaLab/example_clust_bm_plots’s past year of commit activity
    R 0 1 0 0 Updated Dec 16, 2025
  • CimpleG Public

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

    CostaLab/CimpleG’s past year of commit activity
    R 7 GPL-3.0 0 0 0 Updated Dec 5, 2025
  • LR2TF Public
    CostaLab/LR2TF’s past year of commit activity
    R 1 0 0 0 Updated Nov 13, 2025