Pinned Repositories
bamgineer
Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
cbioportal
cBioPortal for Cancer Genomics
ConsensusCruncher
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 consensus sequence.
crescent
The CanceR Single Cell ExpressioN Toolkit one-line-command applications.
fragmentomics
Collection of fragmentomic analysis scripts
inspire-genomics
Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumab
MEDIPIPE
PughLabReadme
Documentation of best practices, coding tips, and ongoing projects developed by the Pugh Lab.
su2c-gsc-scrna
Custom source code used in Richards, Whitley et al., Nature Cancer, 2021
VisCap
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. For algorithmic details, see Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.
Pugh Lab's Repositories
pughlab/fragmentomics
Collection of fragmentomic analysis scripts
pughlab/MEDIPIPE
pughlab/crescent
The CanceR Single Cell ExpressioN Toolkit one-line-command applications.
pughlab/inspire-genomics
Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumab
pughlab/oncographer
OncoGrapher: standardized, graph-based, clinical data abstraction tool leveraging the MOHCCN data standard
pughlab/pipeline-suite
Collection of pipelines for NGS analysis along with utilities
pughlab/ctims
CTIMS project
pughlab/cbioportal-frontend
React Frontend of cBioPortal :tada:
pughlab/HCC_cfMeDIP
pughlab/paper-inspire-cfmedip
Accompanying code for INSPIRE cfMeDIP-seq manuscript
pughlab/ped_CapTCRseq
Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiation
pughlab/TGL49_CHARM_LFS_Fragmentomics
pughlab/cbioportal
cBioPortal for Cancer Genomics
pughlab/cbpOrganizer
Tool to help cbioportal study owners to organize their studies for publishing to cbioportal
pughlab/tigerdb
TIGERdb: T-Cell and ImmunoGlobulin Epitope Receptor DataBase
pughlab/CapTCR-TIL-Tracking
pughlab/cbioportal-docs
pughlab/CNAqc
CNAqc - Copy Number Alteration (CNA) Quality Check package
pughlab/ctims-matchminer-engine
pughlab/ctims-pages
CTIMS Github Pages
pughlab/GSoC
Google Summer of Code Ideas list
pughlab/INSPIRE_TCR
Pan-cancer assessment of the tumour and systemic T-cell receptor repertoire dynamics in patients treated with pembrolizumab
pughlab/IRIS_BulkTCR
pughlab/matchengine-V2
Open source engine for matching cancer patients to precision medicine clinical trials (V2).
pughlab/matchminer-api
A platform for matching patient-specific genomic profiles to precision cancer medicine clinical trials
pughlab/ORACLE_TCR
pughlab/pughLab-softwareHub
pughlab/rascal
R package and Shiny app providing functions for scaling relative copy number to absolute values for shallow whole genome sequencing of cancer samples.
pughlab/SRTPMs
Spatially Resolved Tumor Purity Maps (SRTPMs)
pughlab/TRI_LRWGS_glioma