1 Introduction

canceR is a graphical user friendly interface to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center (cBio) at Memorial-Sloan-Kettering Cancer Center (MSKCC). canceR implements functions from various packages: 1. to acces, explore and extract Genomics Cancers Data Base of MSKCC (cgdsr,(Cerami et al. 2012, @Gao2013)),

  1. to associate phenotypes with gene expression (phenoTest, (Planet 2013)),

  2. to predict which biological process or pathway or immune system are significantly different under the phenotypes and which genes are associated (GSEA-R~[Subramanian2005,Subramanian2007]),

  3. to predict the most up/down regulated gene sets belonging to one of MSigDB collections~[Subramanian2005] (GSEAlm,(Oron, Jiang, and Gentleman 2008)),

  4. to classify genes by diseases (geNetClassifier,(Aibar et al. 2013)), or

  5. to classify genes by variable or phenotype (rpart, (Therneau, Atkinson, and Ripley 2014)),

  6. to plot genes correlations.

  7. to plot survival curves

  8. to plot muti-omics data using Circos style (circlize, (Gu et al. 2014))

2 Installation

2.1 Suplementary librairies (Not R packages)

For Debian distribution (GNU/Linux)

sudo apt-get insall ("r-cran-tcltk2","r-cran-tkrplot")
sudo apt-get install(Tk-table, BWidget)
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install r-cran-xml

For Windows distribution

LibXml2: parser for XML

For OS X distribution XQuartz: graphics device

run R and write theses lines in console to install dependencies.

install.packages("RCurl", "XML")
install.packages(c("cgdsr","tkrplot","Formula","RCurl" ))

2.2 dependencies from Bioconductor

biocManegr::install("GSEABase", "GSEAlm","geNetClassifier","Biobase", "phenoTest")

Get the development version from github


3 Starting Window

run R and write theses lines in console to run canceR package.


The starting window (Figure~@ref(fig:starting.png)-1) loads all available Cancer Studies (Figure~@ref(fig:starting.png)-3) or search some ones by keyword (Figure 1 4). Before to get Cancers Data (Figure 1 7), it is important to set workspace for output files (Figure~@ref(fig:starting.png)-1). The starting window displays Help menu where user can get this vignette (Figure~@ref(fig:starting.png)-2).