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@shahcompbio

ShahCompBio

Computational biology tools from the Shah Lab

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  1. hmmcopy_utils hmmcopy_utils Public

    Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.

    C 39 15

  2. single_cell_pipeline single_cell_pipeline Public

    Single Cell Analysis Automated Workflow

    Python 27 19

  3. spectrum-tme spectrum-tme Public

    Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"

    R 20 8

  4. MultiModalMuSig.jl MultiModalMuSig.jl Public

    A Julia package for extracting mutation signatures using topic models

    Julia 18 4

  5. timescape timescape Public

    Visualization tool for temporal clonal evolution.

    JavaScript 16 6

  6. scvis scvis Public

    Python package for dimension reduction of high-dimensional biological data.

    Python 16 5

Repositories

Showing 10 of 133 repositories
  • shahcompbio/wgs_analysis’s past year of commit activity
    Python 1 1 0 1 Updated Nov 27, 2024
  • SVChordinator Public

    merge, annotate and visualize structural variants

    shahcompbio/SVChordinator’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Nov 25, 2024
  • signals Public

    Single Cell Genomes with Allele Specificity

    shahcompbio/signals’s past year of commit activity
    R 8 1 1 1 Updated Nov 24, 2024
  • shahcompbio/scrna_demultiplexing’s past year of commit activity
    Python 4 MIT 1 0 0 Updated Nov 18, 2024
  • shahcompbio/cellranger_utils’s past year of commit activity
    Python 0 GPL-3.0 1 0 0 Updated Nov 18, 2024
  • doubleTime Public

    doubleTime is a method to estimate the timing of whole-genome doubling event(s) on a clone tree using SNVs

    shahcompbio/doubleTime’s past year of commit activity
    Jupyter Notebook 1 BSD-3-Clause 0 0 0 Updated Nov 15, 2024
  • igver Public

    Automatically take IGV snapshots

    shahcompbio/igver’s past year of commit activity
    Python 1 MIT 0 1 0 Updated Nov 11, 2024
  • wgs Public

    Whole genome workflows

    shahcompbio/wgs’s past year of commit activity
    Python 12 6 0 0 Updated Nov 9, 2024
  • shahcompbio/pypeliner’s past year of commit activity
    Python 2 GPL-3.0 5 0 0 Updated Oct 16, 2024
  • ontmont Public

    ONT split read analysis

    shahcompbio/ontmont’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Oct 2, 2024

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