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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 36 14

  2. single_cell_pipeline single_cell_pipeline Public

    Single Cell Analysis Automated Workflow

    Python 26 18

  3. MultiModalMuSig.jl MultiModalMuSig.jl Public

    A Julia package for extracting mutation signatures using topic models

    Julia 18 4

  4. spectrum-tme spectrum-tme Public

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

    R 17 8

  5. scvis scvis Public

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

    Python 16 5

  6. timescape timescape Public

    Visualization tool for temporal clonal evolution.

    JavaScript 15 6

Repositories

Showing 10 of 131 repositories
  • 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
    Python 1 BSD-3-Clause 0 0 0 Updated Jul 8, 2024
  • bulk-illumina-rnaseq Public Forked from nf-core/rnaseq

    RNA seq analysis pipeline for alignment and quantification of bulk illumina data

    shahcompbio/bulk-illumina-rnaseq’s past year of commit activity
    Nextflow 0 MIT 677 0 0 Updated Jun 29, 2024
  • generate_mafs Public

    Generate Variant Tables from Isabl Results

    shahcompbio/generate_mafs’s past year of commit activity
    Python 0 1 0 0 Updated Jun 27, 2024
  • ontmont Public

    ONT split read analysis

    shahcompbio/ontmont’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Jun 17, 2024
  • oncokb-annotation Public

    Simple script to annotate variants using oncokb

    shahcompbio/oncokb-annotation’s past year of commit activity
    Shell 0 0 0 0 Updated May 31, 2024
  • nanoseq Public Forked from apsteinberg/nanoseq

    Nanopore demultiplexing, QC and alignment pipeline

    shahcompbio/nanoseq’s past year of commit activity
    Nextflow 0 MIT 76 0 0 Updated May 28, 2024
  • signals Public

    Single Cell Genomes with Allele Specificity

    shahcompbio/signals’s past year of commit activity
    R 7 1 1 1 Updated May 22, 2024
  • shahcompbio/scrna_demultiplexing’s past year of commit activity
    Python 4 MIT 0 0 0 Updated May 21, 2024
  • gdan-sv-consensus Public

    Getting GDAN SV consensus based on bedpe files

    shahcompbio/gdan-sv-consensus’s past year of commit activity
    Python 1 0 0 0 Updated Apr 19, 2024
  • shahcompbio/cellranger_utils’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Apr 18, 2024

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