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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 44 14

  2. single_cell_pipeline single_cell_pipeline Public

    Single Cell Analysis Automated Workflow

    Python 28 19

  3. spectrum-tme spectrum-tme Public

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

    R 24 8

  4. MultiModalMuSig.jl MultiModalMuSig.jl Public

    A Julia package for extracting mutation signatures using topic models

    Julia 19 4

  5. timescape timescape Public

    Visualization tool for temporal clonal evolution.

    JavaScript 18 6

  6. scvis scvis Public

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

    Python 16 5

Repositories

Showing 10 of 162 repositories
  • signals Public

    Single Cell Genomes with Allele Specificity

    shahcompbio/signals’s past year of commit activity
    R 11 1 2 0 Updated Jan 28, 2026
  • nanogenome Public

    Long-read DNA variant and mobile element analysis

    shahcompbio/nanogenome’s past year of commit activity
    Nextflow 0 MIT 1 0 0 Updated Jan 28, 2026
  • chromoscope Public Forked from hms-dbmi/chromoscope

    Interactive multiscale visualization for structural variation in human genomes

    shahcompbio/chromoscope’s past year of commit activity
    TypeScript 0 MIT 7 0 0 Updated Jan 15, 2026
  • spectrum_cfdna_figures Public

    Repo to reproduce figures from Williams et al. 2025

    shahcompbio/spectrum_cfdna_figures’s past year of commit activity
    R 1 MIT 0 0 0 Updated Jan 9, 2026
  • minda Public Forked from KolmogorovLab/minda
    shahcompbio/minda’s past year of commit activity
    Python 0 4 0 0 Updated Jan 8, 2026
  • SVChordinator Public

    merge, annotate and visualize structural variants

    shahcompbio/SVChordinator’s past year of commit activity
    Python 0 Apache-2.0 0 0 1 Updated Jan 4, 2026
  • proteomegenerator3 Public

    Generate proteogenomics search databases from long-read RNAseq

    shahcompbio/proteomegenerator3’s past year of commit activity
    Nextflow 0 MIT 1 0 0 Updated Dec 3, 2025
  • HMMclone Public

    Calling copy number in pseudobulk clones

    shahcompbio/HMMclone’s past year of commit activity
    R 2 0 0 0 Updated Dec 3, 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 Nov 13, 2025
  • peptidescope Public

    visualize MS peptides with transcript structures

    shahcompbio/peptidescope’s past year of commit activity
    Perl 0 1 0 0 Updated Oct 30, 2025

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