gnomeR R package

Please find all the package’s resources on it’s github repository.

Introduction

The gnomeR package provides a consistent framework for genetic data processing, visualization and analysis. This is primarily targeted to IMPACT datasets but can also be applied to any genomic data provided by CbioPortal.

• Dowloading and gathering data from CbioPortal through an integrated API using simply the sample IDs of the samples of interests or the name of the study to retrive all samples in that study. A separate package cbioportalr was developed independently.
• Processing genomic data retrieved for mutations (MAF file), fusions (MAF file) and copy-number alterations (and when available segmentation files) into an analysis ready format.
• Visualization of the processed data provided through MAF file summaries, OncoPrints and heatmaps.
• Analyzing the processed data for association with binary, continuous and survival outcome. Including further visualiztion to improve understanding of the results.

Installation

You can install gnomeR from GitHub with:

# install.packages("devtools")
devtools::install_github("AxelitoMartin/gnomeR")

Similarly for those who wish to explore the development version of gnomeR:

devtools::install_github("AxelitoMartin/gnomeR", ref = "development")

Along with its companion package for cbioPortal data download:

devtools::install_github("karissawhiting/cbioportalr")