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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 20

  3. spectrum-tme spectrum-tme Public

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

    R 21 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 140 repositories
  • igver Public

    Automatically take IGV snapshots

    shahcompbio/igver’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Feb 24, 2025
  • ArtiCull Public
    shahcompbio/ArtiCull’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 24, 2025
  • spectrum-tme Public

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

    shahcompbio/spectrum-tme’s past year of commit activity
    R 21 8 1 0 Updated Feb 22, 2025
  • nanoseq Public Forked from apsteinberg/nanoseq

    Nanopore demultiplexing, QC and alignment pipeline

    shahcompbio/nanoseq’s past year of commit activity
    Nextflow 0 MIT 83 0 0 Updated Feb 21, 2025
  • proteomegenerator-smk Public

    Snakemake workflow for proteomegenerator Isabl app

    shahcompbio/proteomegenerator-smk’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 17, 2025
  • transdecoder-smk Public

    snakemake pipeline for transdecoder

    shahcompbio/transdecoder-smk’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 17, 2025
  • bambu-smk Public

    Snakemake workflow for transcript assembly with Bambu

    shahcompbio/bambu-smk’s past year of commit activity
    R 0 MIT 0 0 0 Updated Feb 14, 2025
  • driver-concordance Public

    A pipeline to process CN and VCF data between paired samples to calculate driver event concordance

    shahcompbio/driver-concordance’s past year of commit activity
    Python 0 0 0 0 Updated Feb 14, 2025
  • rustbam Public

    Rust-powered BAM depth extraction with Python bindings

    shahcompbio/rustbam’s past year of commit activity
    Rust 0 MIT 0 0 0 Updated Feb 10, 2025
  • 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 Jan 28, 2025

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