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  1. hotnet2 hotnet2 Public

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

    Python 98 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 66 31

  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 82 repositories
  • 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 Sep 9, 2024
  • MOLLUSC Public

    Maximum Likelihood Estimation Of Lineage and Location Using Single Cell Spatial Lineage tracing Data

    raphael-group/MOLLUSC’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Sep 4, 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 8 BSD-3-Clause 2 0 2 Updated Sep 4, 2024
  • startle Public
    raphael-group/startle’s past year of commit activity
    C++ 4 MIT 1 0 0 Updated Sep 4, 2024
  • copulacci Public
    raphael-group/copulacci’s past year of commit activity
    Jupyter Notebook 3 0 1 0 Updated Sep 4, 2024
  • MERLIN Public
    raphael-group/MERLIN’s past year of commit activity
    Python 4 0 1 0 Updated Aug 29, 2024
  • paste3 Public
    raphael-group/paste3’s past year of commit activity
    Python 0 BSD-3-Clause 0 4 0 Updated Aug 29, 2024
  • GASTON Public
    raphael-group/GASTON’s past year of commit activity
    Python 14 BSD-3-Clause 4 0 0 Updated Aug 29, 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 66 BSD-3-Clause 31 51 4 Updated Aug 28, 2024
  • fastBE Public
    raphael-group/fastBE’s past year of commit activity
    Jupyter Notebook 5 0 0 0 Updated Aug 25, 2024
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