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Popular repositories

  1. hotnet2 hotnet2 Public

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

    Python 96 43

  2. paste paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 71 17

  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 70 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 56 27

  5. hierarchical-hotnet hierarchical-hotnet Public

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

    Python 36 23

  6. chisel chisel Public

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

    Python 36 11

Repositories

Showing 10 of 80 repositories
  • CalicoST Public

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

    Python 4 BSD-3-Clause 2 1 0 Updated Apr 18, 2024
  • LAML Public

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

    Python 2 GPL-3.0 0 0 0 Updated Apr 18, 2024
  • laml-experiments Public

    experiments for the LAML paper

    Jupyter Notebook 0 0 0 0 Updated Apr 16, 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.

    Roff 56 BSD-3-Clause 27 50 3 Updated Apr 16, 2024
  • DeST_OT Public

    Developmental Spatiotemporal Optimal Transport

    Jupyter Notebook 2 BSD-3-Clause 0 0 0 Updated Apr 14, 2024
  • GASTON Public
    Python 9 BSD-3-Clause 1 0 0 Updated Apr 9, 2024
  • sc-mail-experiments Public
    Jupyter Notebook 0 0 0 0 Updated Apr 8, 2024
  • copulacci Public
    Jupyter Notebook 1 0 0 0 Updated Apr 2, 2024
  • hatchet2-simulations Public

    Snakemake pipeline for generating and running on new simulated data for HATCHet2 revisions

    Python 0 BSD-3-Clause 0 0 0 Updated Apr 2, 2024
  • hatchet2-paper Public

    Publication repository for results that accompany the HATCHet2 paper.

    0 BSD-3-Clause 0 0 0 Updated Apr 2, 2024
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