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cancerGI
View on CRAN: Click
here
Download and install cancerGI package within the R console
Install from CRAN:
install.packages("cancerGI")
Install from Github:
library("remotes")
install_github("cran/cancerGI")
Install by package version:
library("remotes")
install_version("cancerGI", "1.0.1")
Attach the package and use:
library("cancerGI")
Maintained by
Audrey Q. Fu
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-04-01
Latest Update: 2023-09-07
Description:
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. .
How to cite:
Audrey Q. Fu (2016). cancerGI: Analyses of Cancer Gene Interaction. R package version 1.0.1, https://cran.r-project.org/web/packages/cancerGI. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.0.0 (2016-04-01 16:42)
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Complete documentation for cancerGI
Functions, R codes and Examples using
the cancerGI R package
Some associated functions: RNAi . computeSmallWorldness . computeSurvivalPValueForGenePairSet.output . computeSurvivalPValueGenePairAll.output . computeSurvivalPValueOneGenePair . computeSurvivalPValueOneGenePair.output . constructDesignMatrix . mutations . processDataMutSurv . survival . testMutationalPatternAll.wrapper . tested_pairs .
Some associated R codes: computeSmallWorldness.R . computeSurvivalPValueForGenePairSet.output.R . computeSurvivalPValueGenePairAll.R . computeSurvivalPValueGenePairAll.output.R . computeSurvivalPValueOneGenePair.R . computeSurvivalPValueOneGenePair.output.R . constructDesignMatrix.R . findSurvMedian.R . processDataMutSurv.R . testMutationalPatternAll.R . testMutationalPatternAll.wrapper.R . testMutationalPatternBinom.R . testMutationalPatternPair.R . Full cancerGI package functions and examples
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