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  1. hotnet2 hotnet2 Public

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

    Python 100 43

  2. paste paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 80 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 71 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. chisel chisel Public

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

    Python 37 11

  6. hierarchical-hotnet hierarchical-hotnet Public

    Hierarchical HotNet is an algorithm for finding hierarchies of active subnetworks.

    Python 36 23

Repositories

Showing 10 of 88 repositories
  • chimeric-epistasis Public
    raphael-group/chimeric-epistasis’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Dec 12, 2024
  • dialect Public
    raphael-group/dialect’s past year of commit activity
    Jupyter Notebook 4 BSD-3-Clause 0 0 0 Updated Dec 12, 2024
  • 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 24 BSD-3-Clause 3 2 4 Updated Dec 12, 2024
  • paste3 Public
    raphael-group/paste3’s past year of commit activity
    Python 1 BSD-3-Clause 1 9 0 Updated Dec 3, 2024
  • 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 69 BSD-3-Clause 32 56 6 Updated Nov 27, 2024
  • raphael-group.github.io Public

    Raphael group website.

    raphael-group/raphael-group.github.io’s past year of commit activity
    HTML 0 2 0 0 Updated Nov 24, 2024
  • 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 5 BSD-3-Clause 0 0 0 Updated Nov 22, 2024
  • MERLIN Public
    raphael-group/MERLIN’s past year of commit activity
    Python 7 0 2 0 Updated Nov 19, 2024
  • FRLC Public

    Low-rank optimal transport through factor relaxation with latent coupling.

    raphael-group/FRLC’s past year of commit activity
    Jupyter Notebook 3 0 0 0 Updated Nov 13, 2024
  • chisel Public

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

    raphael-group/chisel’s past year of commit activity
    Python 37 BSD-3-Clause 11 6 1 Updated Nov 13, 2024
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