Pugh Lab

fragmentomics

Collection of fragmentomic analysis scripts

MEDIPIPE

crescent

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

inspire-genomics

Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumab

LFS-early-detection-ctdna

Multi-modal analysis of cell-free DNA for the early detection of cancer in Li-Fraumeni syndrome.

oncographer

pipeline-suite

Collection of pipelines for NGS analysis along with utilities

ctims

CTIMS project

cbioportal-frontend

React Frontend of cBioPortal :tada:

HCC_cfMeDIP

mcoder

paper-inspire-cfmedip

Accompanying code for INSPIRE cfMeDIP-seq manuscript

ped_CapTCRseq

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

TGL49_CHARM_LFS_Fragmentomics

cbioportal

cBioPortal for Cancer Genomics

cbpOrganizer

Tool to help cbioportal study owners to organize their studies for publishing to cbioportal

EVOLVE_ctDNA

code used for the analysis and visualization of the EVOLVE ctDNA project

CapTCR-TIL-Tracking

cbioportal-docs

CNAqc

CNAqc - Copy Number Alteration (CNA) Quality Check package

ctims-pages

CTIMS Github Pages

GSoC

Google Summer of Code Ideas list

INSPIRE_TCR

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

IRIS_BulkTCR

matchengine-V2

Open source engine for matching cancer patients to precision medicine clinical trials (V2).

matchminer-api

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

ORACLE_TCR

pughLab-softwareHub

rascal

R package and Shiny app providing functions for scaling relative copy number to absolute values for shallow whole genome sequencing of cancer samples.

SRTPMs

Spatially Resolved Tumor Purity Maps (SRTPMs)