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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 20 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 11

  5. crescent crescent Public

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

    R 9 4

  6. pipeline-suite pipeline-suite Public

    Collection of pipelines for NGS analysis along with utilities

    Perl 4 3

Repositories

Showing 10 of 124 repositories
  • mixcr_QC Public
    pughlab/mixcr_QC's past year of commit activity
    Python 0 1 0 0 Updated Sep 23, 2026
  • ctims-matchminer-engine Public
    pughlab/ctims-matchminer-engine's past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Sep 21, 2026
  • 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 MIT 1 0 0 Updated Sep 9, 2026
  • ctims Public

    CTIMS project

    pughlab/ctims's past year of commit activity
    CSS 3 Apache-2.0 10 8 5 Updated Aug 19, 2026
  • tigerdb Public

    TIGERdb: T-Cell and ImmunoGlobulin Epitope Receptor DataBase

    pughlab/tigerdb's past year of commit activity
    TypeScript 1 AGPL-3.0 0 0 3 Updated Aug 19, 2026
  • ped_CapTCRseq Public

    Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiation

    pughlab/ped_CapTCRseq's past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Aug 6, 2026
  • EAC-ML-pipeline Public

    This directory contains scripts for "Tumor-agnostic multimodal blood cell-free DNA analysis enables detection, monitoring, and risk stratification in esophageal adenocarcinoma " by Bartolomucci1 et al., 2026

    pughlab/EAC-ML-pipeline's past year of commit activity
    0 0 0 0 Updated Jul 29, 2026
  • cfdna-myeloma-multiomics Public

    Analysis and manuscript code for a targeted panel and shallow WGS study of peripheral blood and bone marrow cell-free DNA in multiple myeloma. Includes pipelines for feature processing (mutations, translocations, CNAs, BCR, fragmentomics), integration across cohorts, longitudinal tracking, and modeling of MRD/progression.

    pughlab/cfdna-myeloma-multiomics's past year of commit activity
    R 0 0 0 0 Updated Jul 24, 2026
  • oncographer Public

    OncoGrapher: standardized, graph-based, clinical data abstraction tool leveraging the MOHCCN data standard

    pughlab/oncographer's past year of commit activity
    TypeScript 5 1 0 0 Updated Jul 7, 2026
  • MismatchResolveDX Public

    This pipeline is used for the analysis of the MismatchResolveDx (previously the MultiMMR) sequencing panel (including shallow WGS and targeted sequencing of conventional DNA and methylation sites).

    pughlab/MismatchResolveDX's past year of commit activity
    Perl 0 1 0 0 Updated May 27, 2026
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