In mil2041/CNCDriver: CNCDriver

library(knitr)
opts_chunk$set(out.extra='style="display:block; margin: auto"', fig.align="center", fig.width=12, fig.height=12, tidy=TRUE)

BiocStyle::markdown()

Overview

The CNCDriver combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers

Basics

Installation

library(remotes)
install_github(repo="khuranalab/CNCDriver", ref="master", build_vignette=TRUE)

Getting Started

Load CNCDriver package:

library(CNCDriver)

A list of all accessible vignettes and methods is available with the following command:

help.search("CNCDriver")

For help on any CNCDriver package functions, use one of the following command formats:

help(getCDSPvalue)
?getCDSPvalue

Load FunSeq2 annotations of WGS SNV mutation calls in LGG.

Load pre-parsed FunSeq2 annotations of WGS SNV mutation calls in BRCA. The whole genome sequencing SNV mutation calls in BRCA are from Fredriksson et al. Nature Genetics 2015. WGS SNV data is available at

# Load pre-parsed FunSeq2 annotations for SNV mutation calls in LGG.
data("reducedFunseqOutputCDS")
data("reducedFunseqOutputNCDS")

References

Eric Minwei Liu, Alexander Martinez Fundichely, Bianca Jay Diaz, Boaz Aronson, Tawny Cuykendall, Matthew MacKay, Priyanka Dhingra, Elissa WP Wong, Ping Chi, Effie Apostolou, Neville E Sanjana, Ekta Khurana “Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes”, Cell Systems, 8,4460455. e8 (2019)