cancerGI: Analyses of Cancer Gene Interaction

Functions to perform the following analyses: i) inferring epistasis from RNAi double knockdown data; ii) identifying gene pairs of multiple mutation patterns; iii) assessing association between gene pairs and survival; and iv) calculating the smallworldness of a graph (e.g., a gene interaction network). Data and analyses are described in Wang, X., Fu, A. Q., McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast cancer genes. Nature Communications. 5 4828. <doi:10.1038/ncomms5828>.

Version: 1.0.0
Depends: R (≥ 2.10)
Imports: systemfit, qvalue, survival, reshape2, igraph
Published: 2016-04-01
Author: Audrey Qiuyan Fu and Xiaoyue Wang
Maintainer: Audrey Q. Fu <audreyqyfu at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: cancerGI results

Downloads:

Reference manual: cancerGI.pdf
Package source: cancerGI_1.0.0.tar.gz
Windows binaries: r-devel: cancerGI_1.0.0.zip, r-release: cancerGI_1.0.0.zip, r-oldrel: cancerGI_1.0.0.zip
OS X Mavericks binaries: r-release: cancerGI_1.0.0.tgz, r-oldrel: cancerGI_1.0.0.tgz

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