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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 96 19

  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 73 33

  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 31

  5. GASTON GASTON Public

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

    Python 63 11

  6. chisel chisel Public

    CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links

    Python 43 14

Repositories

Showing 10 of 93 repositories
  • 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 12, 2025
  • 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 Nov 5, 2025
  • GASTON-Mix Public
    raphael-group/GASTON-Mix’s past year of commit activity
    Python 10 BSD-3-Clause 0 1 0 Updated Oct 16, 2025
  • HiRef Public

    Hierarchical Refinement: Optimal Transport to Infinity and Beyond

    raphael-group/HiRef’s past year of commit activity
    Jupyter Notebook 12 1 0 0 Updated Sep 29, 2025
  • LAML Public

    LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data

    raphael-group/LAML’s past year of commit activity
    Python 11 BSD-3-Clause 1 2 0 Updated Sep 23, 2025
  • HM-OT Public

    Hidden Markov Optimal Transport: learning the sequence of latent cell-states and transitions in transcriptomic time-series.

    raphael-group/HM-OT’s past year of commit activity
    Jupyter Notebook 9 0 0 0 Updated Aug 24, 2025
  • CalicoST Public

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

    raphael-group/CalicoST’s past year of commit activity
    Python 42 BSD-3-Clause 4 8 4 Updated Aug 19, 2025
  • raphael-group/chimeric-epistasis’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Aug 4, 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 63 BSD-3-Clause 11 0 1 Updated Jun 17, 2025
  • Multi-GASTON Public
    raphael-group/Multi-GASTON’s past year of commit activity
    Python 7 BSD-3-Clause 0 0 0 Updated Jun 6, 2025

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