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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 77 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 68 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
  • paste3 Public
    raphael-group/paste3’s past year of commit activity
    Python 0 BSD-3-Clause 1 6 2 Updated Nov 13, 2024
  • FRLC Public

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

    raphael-group/FRLC’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Nov 10, 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 8, 2024
  • raphael-group/tree-labeling-polytope’s past year of commit activity
    Python 0 0 0 0 Updated Nov 5, 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 4, 2024
  • SIID Public

    Joint imputation and deconvolution across two spatial datasets

    raphael-group/SIID’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Nov 4, 2024
  • dialect Public
    raphael-group/dialect’s past year of commit activity
    Jupyter Notebook 3 0 0 0 Updated Oct 31, 2024
  • raphael-group/GASTON-Mix’s past year of commit activity
    Python 0 0 0 0 Updated Oct 30, 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 Oct 30, 2024
  • 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 1 0 0 0 Updated Oct 29, 2024

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