Skip to content
@shahcompbio

ShahCompBio

Computational biology tools from the Shah Lab

Popular repositories Loading

  1. hmmcopy_utils hmmcopy_utils Public

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

    C 41 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 161 repositories
  • nanogenome Public

    Long-read DNA variant and mobile element analysis

    shahcompbio/nanogenome’s past year of commit activity
    Nextflow 0 MIT 0 0 1 Updated Nov 20, 2025
  • 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 Nov 18, 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
  • minda Public Forked from KolmogorovLab/minda
    shahcompbio/minda’s past year of commit activity
    Python 0 4 0 0 Updated Nov 5, 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
  • ORFology Public

    protein annotation based on sequence composition

    shahcompbio/ORFology’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 20, 2025
  • tcdo_pg_tools Public

    Commandline tools to support proteogenomics analyses at MSK TCDO and beyond

    shahcompbio/tcdo_pg_tools’s past year of commit activity
    Python 0 0 0 0 Updated Oct 20, 2025
  • 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 Oct 7, 2025
  • wakcna Public

    long-read copy number analysis from phased SVs using Wakhan

    shahcompbio/wakcna’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 6, 2025
  • nanoseq Public Forked from apsteinberg/nanoseq

    Nanopore demultiplexing, QC and alignment pipeline

    shahcompbio/nanoseq’s past year of commit activity
    Nextflow 0 MIT 101 0 1 Updated Sep 6, 2025