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@pughlab

Pugh Lab

The Pugh Laboratory at the Princess Margaret Cancer Centre

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  1. PughLabReadme PughLabReadme Public

    Documentation of best practices, coding tips, and ongoing projects developed by the Pugh Lab.

    1

  2. cbioportal cbioportal Public

    Forked from cBioPortal/cbioportal

    cBioPortal for Cancer Genomics

    Java 2

  3. ConsensusCruncher ConsensusCruncher Public

    ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a cons…

    Jupyter Notebook 21 9

  4. VisCap VisCap Public

    VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data.…

    R 22 12

  5. crescent crescent Public

    The CanceR Single Cell ExpressioN Toolkit one-line-command applications.

    R 8 4

  6. pipeline-suite pipeline-suite Public

    Collection of pipelines for NGS analysis along with utilities

    Perl 4 3

Repositories

Showing 10 of 115 repositories
  • matchminer-api Public Forked from dfci/matchminer-api

    A platform for matching patient-specific genomic profiles to precision cancer medicine clinical trials

    pughlab/matchminer-api’s past year of commit activity
    Python 0 13 0 2 Updated Sep 20, 2025
  • ctims-matchminer-engine Public
    pughlab/ctims-matchminer-engine’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Sep 18, 2025
  • ctims Public

    CTIMS project

    pughlab/ctims’s past year of commit activity
    CSS 3 Apache-2.0 10 8 4 Updated Sep 15, 2025
  • pipeline-suite Public

    Collection of pipelines for NGS analysis along with utilities

    pughlab/pipeline-suite’s past year of commit activity
    Perl 4 3 0 0 Updated Sep 5, 2025
  • tigerdb Public

    TIGERdb: T-Cell and ImmunoGlobulin Epitope Receptor DataBase

    pughlab/tigerdb’s past year of commit activity
    TypeScript 1 0 0 1 Updated Aug 28, 2025
  • cfWGS-MM-MRD Public Forked from DoryAbelman/cfWGS-MM-MRD

    This directory contains scripts for "Cell-free DNA Whole Genome Sequencing for Non-Invasive MRD Detection in Multiple Myeloma" by Abelman et al., 2025

    pughlab/cfWGS-MM-MRD’s past year of commit activity
    R 0 1 0 0 Updated Aug 27, 2025
  • INSPIRE_TCR Public

    Pan-cancer assessment of the tumour and systemic T-cell receptor repertoire dynamics in patients treated with pembrolizumab

    pughlab/INSPIRE_TCR’s past year of commit activity
    R 2 0 0 0 Updated Aug 20, 2025
  • CompareFragmentSize Public

    Compare fragment size of variant- and reference-allele containing reads in a BAM file

    pughlab/CompareFragmentSize’s past year of commit activity
    R 0 GPL-3.0 0 0 0 Updated May 26, 2025
  • crescent Public

    The CanceR Single Cell ExpressioN Toolkit one-line-command applications.

    pughlab/crescent’s past year of commit activity
    R 8 GPL-3.0 4 1 0 Updated May 14, 2025
  • MEDIPIPE Public
    pughlab/MEDIPIPE’s past year of commit activity
    HTML 11 MIT 4 0 0 Updated May 13, 2025
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