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@cantinilab

Machine Learning for Integrative Genomics lab

README.md

Machine Learning for Integrative Genomics (ML4IG)

Summary

We are a G5 research group led by Laura Cantini (@laucan88) and located at the Institut Pasteur (Paris, FR).

We work at the interphase of machine learning and genomics, developing methods exploiting the full richness and complementarity of the available single-cell data to derive actionable biological knowledge.

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  1. momix-notebook momix-notebook Public

    Jupyter Notebook 60 11

  2. Mowgli Mowgli Public

    Single-cell multi-omics integration using Optimal Transport

    Python 37 2

  3. HuMMuS HuMMuS Public

    Molecular interactions inference from single-cell multi-omics data

    R 18 4

  4. scconfluence scconfluence Public

    A novel method for single-cell diagonal integration: scConfluence

    Python 11

  5. scNET scNET Public

    jupyther notebook comparing reproducibility of single-cell network inference algorithms

    Jupyter Notebook 4 2

  6. mowgli_reproducibility mowgli_reproducibility Public

    Data and scripts to reproduce experiments for Mowgli.

    Python 3 1

Repositories

Showing 10 of 17 repositories
  • scPRINT Public Forked from jkobject/scPRINT

    single cell foundation model for Gene network inference and more

    cantinilab/scPRINT’s past year of commit activity
    Jupyter Notebook 10 GPL-3.0 1 1 (1 issue needs help) 0 Updated Sep 19, 2024
  • .github Public

    home page

    cantinilab/.github’s past year of commit activity
    0 0 0 0 Updated Sep 18, 2024
  • scPRINT-old1 Public archive

    Single Cell Pretrained Regulatory network INference from Transcripts

    cantinilab/scPRINT-old1’s past year of commit activity
    Jupyter Notebook 11 GPL-3.0 1 0 0 Updated Sep 17, 2024
  • scDataLoader Public Forked from jkobject/scDataLoader

    a dataloader to work with large single cell datasets from lamindb

    cantinilab/scDataLoader’s past year of commit activity
    Jupyter Notebook 0 GPL-3.0 2 0 0 Updated Sep 16, 2024
  • Mowgli Public

    Single-cell multi-omics integration using Optimal Transport

    cantinilab/Mowgli’s past year of commit activity
    Python 37 GPL-3.0 2 4 0 Updated Sep 6, 2024
  • GRnnData Public

    Awesome GRN enhanced AnnData toolkit

    cantinilab/GRnnData’s past year of commit activity
    Jupyter Notebook 1 GPL-3.0 1 0 2 Updated Sep 5, 2024
  • benGRN Public Forked from jkobject/benGRN

    Awesome Benchmark of Gene Regulatory Networks

    cantinilab/benGRN’s past year of commit activity
    Jupyter Notebook 0 GPL-3.0 1 0 0 Updated Sep 5, 2024
  • stories Public

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

    cantinilab/stories’s past year of commit activity
    Python 8 GPL-3.0 0 0 0 Updated Aug 21, 2024
  • HuMMuS Public

    Molecular interactions inference from single-cell multi-omics data

    cantinilab/HuMMuS’s past year of commit activity
    R 18 AGPL-3.0 4 1 0 Updated Aug 9, 2024
  • Circe Public

    Co-accessibility network from ATAC-seq data. Python code, based on Cicero package (R).

    cantinilab/Circe’s past year of commit activity
    Python 13 AGPL-3.0 0 0 0 Updated Jul 22, 2024
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