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As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of …
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README.rst

PPTC PDX Oncoprint Generation

Authors: Jo Lynne Rokita
Alvin Farrel
Khushbu Patel
Contact: Jo Lynne Rokita (rokita@email.chop.edu)
Organization: CHOP
Status: In-process
Date: 2019-07-18

Introduction

Here, we provide scripts to enable reproducible generation of Manuscript Figure 2: oncoprints by PDX histology. This repo contains code for:

  1. Create expanded oncoprint matrices used to reproduce Figure 2

Details

  • data-fetch-pptc-pdx-oncoprints.sh
  • RUN-create-full-oncoprint.R
  • install-packages.R
  • demog-color-function.R
  • mutation-color-function.R
  • reformat-fusion-as-matrix.R
  • load-maf-maftools.R
  • create-mut-sigs-matrix.R
  • create-mut-matrices.R
  • create-CN-matrices.R
  • merge-mut-CN-matrices.R
  • merge-CN-gistic-matrices-new.R
  • create-complexheat-oncoprint-all.R
  • merge-mut-CN-fusion-matrices.R

Software Requirements

R 3.4.3

Pipeline

# How to run:
# Download github repository in your home directory (~/)
# Make sure to not clone the repository inside any other repository in your home directory
git clone https://github.com/marislab/create-pptc-pdx-oncoprints.git

# Run script to fetch data files
./data-fetch-pptc-pdx-oncoprints.sh

# Run script to generate oncoprints
Rscript RUN-create-full-oncoprint.R
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