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  1. hotnet2 hotnet2 Public

    HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network

    Python 102 43

  2. paste paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 100 20

  3. THetA THetA Public

    Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This re…

    Python 76 29

  4. hatchet hatchet Public

    HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, a…

    Roff 70 32

  5. GASTON GASTON Public

    GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data

    Python 70 15

  6. CalicoST CalicoST Public

    Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

    Python 46 4

Repositories

Showing 10 of 98 repositories
  • hatchet Public

    HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

    raphael-group/hatchet’s past year of commit activity
    Roff 70 BSD-3-Clause 32 56 5 Updated Feb 14, 2026
  • LAML-Pro Public
    raphael-group/LAML-Pro’s past year of commit activity
    C++ 0 1 0 0 Updated Feb 6, 2026
  • MET-MAP Public

    Reproducibility repository for Multi-GASTON applied on spatial metabolomics data

    raphael-group/MET-MAP’s past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 0 0 0 Updated Dec 5, 2025
  • Multi-GASTON Public
    raphael-group/Multi-GASTON’s past year of commit activity
    Python 7 BSD-3-Clause 1 0 0 Updated Dec 5, 2025
  • GASTON Public

    GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data

    raphael-group/GASTON’s past year of commit activity
    Python 70 BSD-3-Clause 15 0 1 Updated Dec 1, 2025
  • LAML-Pro-experiments Public
    raphael-group/LAML-Pro-experiments’s past year of commit activity
    HTML 0 0 0 0 Updated Nov 29, 2025
  • troupe Public

    Code for Tree-informed Rate Optimization Using Potency Enforcement and associated experiments

    raphael-group/troupe’s past year of commit activity
    Python 1 0 0 0 Updated Nov 22, 2025
  • MGW Public
    raphael-group/MGW’s past year of commit activity
    Python 4 1 0 0 Updated Nov 22, 2025
  • MOSAICField Public

    Source code for MOSAICField multimodal spatial alignment and morphological mapping

    raphael-group/MOSAICField’s past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 1 0 0 Updated Nov 21, 2025
  • Phyllochron Public

    Phyllochron is an ILP method that solves the Maximum Likelihood Longitudinal Assignment Problem under the Longitudinally Observed Perfect Phylogeny Model.

    raphael-group/Phyllochron’s past year of commit activity
    Jupyter Notebook 2 MIT 0 0 0 Updated Nov 20, 2025
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