pughlab/BCa_ATACSEQ_Project

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pughlab/BCa_ATACSEQ_Project

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This repository contains custom code used for analysis in El Ghamrasni et al.,

bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

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.

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.

Jupyter Notebook

MEDIPIPE

fragmentomics

Collection of fragmentomic analysis scripts

su2c-gsc-scrna

Custom source code used in Richards, Whitley et al., Nature Cancer, 2021

Jupyter Notebook

inspire-genomics

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

crescent

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

crescent-frontend

CReSCENT Portal: https://crescent.cloud | CReSCENT Docs: https://pughlab.github.io/crescent-frontend/

LFS-early-detection-ctdna

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

oncographer

tracker

Generic research tracking system

inspire-ctdna

Custom R scripts for data visualization and statistical analysis for Bratman, Yang et al. 2020 Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab

cancer-scrna-integration

A comparison of data integration methods for single-cell RNA sequencing of cancer samples

Jupyter Notebook

cfMeDIP-seq-analysis-pipeline

Post-processing pipeline for next-generation circulating methylome data generated by cfMeDIP-seq

pipeline-suite

Collection of pipelines for NGS analysis along with utilities

LB-Seq

Liquid Biopsy Sequencing analysis tools for cell free DNA sequencing

VisCapCancer

Tool for calling tumour-specific somatic copy number alterations from targeted sequencing data. This tool is based on the germline copy number variant caller published by Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

scVkMYC_mPC

TGL48_Uveal_Melanoma

scripts for uveal paper

PughLabReadme

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

ctims

ped_CapTCRseq

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

Jupyter Notebook

wnt-medulloblastoma-singh

Code for scRNAseq analysis in Manoranjan et al., Nature Communications, 2020

Jupyter Notebook

cbio_import_utils

ddx56-pearson-lab

Code for scRNAseq analysis in Pryszlak et al., Cell Reports, 2021

Jupyter Notebook

Clump

net-seq

mcoder

HCC_cfMeDIP

TGL49_CHARM_LFS_Fragmentomics

cfmedip_analysis

Pre-processing pipeline to transform MEDIPS output wig files into matrix of chromosomal bins by samples

btsc-glutaminase-weiss

Code for scRNAseq analysis in Restall et al., Cancer Research, 2020

paper-inspire-cfmedip

Accompanying code for INSPIRE cfMeDIP-seq manuscript