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  1. hotnet2 hotnet2 Public

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

    Python 101 43

  2. paste paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 87 18

  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 72 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 69 32

  5. GASTON GASTON Public

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

    Python 48 5

  6. chisel chisel Public

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

    Python 38 11

Repositories

Showing 10 of 93 repositories
  • HM-OT Public

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

    Jupyter Notebook 2 0 0 0 Updated Apr 22, 2025
  • HiRef Public

    Hierarchical Refinement: Optimal Transport to Infinity and Beyond

    Jupyter Notebook 2 0 0 0 Updated Apr 20, 2025
  • CalicoST Public

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

    Python 34 BSD-3-Clause 3 4 4 Updated Apr 17, 2025
  • Phyllochron Public

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

    Jupyter Notebook 1 MIT 0 0 0 Updated Apr 15, 2025
  • raphael-group.github.io Public

    Raphael group website.

    HTML 0 2 0 0 Updated Apr 11, 2025
  • dialog Public
    Python 0 BSD-3-Clause 0 0 0 Updated Apr 7, 2025
  • dialect Public
    Python 4 BSD-3-Clause 0 0 0 Updated Apr 3, 2025
  • fastBE Public

    ultrafast phylogenetic reconstruction from bulk DNA sequencing data

    Jupyter Notebook 5 0 0 0 Updated Apr 1, 2025
  • LAML Public

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

    Python 6 BSD-3-Clause 1 1 0 Updated Mar 28, 2025
  • Python 0 0 0 0 Updated Mar 21, 2025