This package implements methods to analyze and visualize expression data.
So far, it is only implemented for human and mouse data!
It uses function from the following packages:
Dr. Shirin Glander
# install package from github
install.packages("devtools")
library(devtools)
# either the latest stable release that passed TRAVIS CI check
devtools::install_github("ShirinG/exprAnalysis", build_vignettes=TRUE, ref = "stable.version0.1.0")
# or the development version
devtools::install_github("ShirinG/exprAnalysis", build_vignettes=TRUE, ref = "master")
There might be problems with installation of some dependency packages (especially Bioconductor packages and WGCNA and its dependencies from CRAN). In order to install them manually:
list.of.packages_bioconductor <- c("arrayQualityMetrics", "beadarray", "pcaGoPromoter", "limma", "pathview", "sva", "GO.db", "impute")
list.of.packages_cran <- c("WGCNA", "roxygen2", "testthat", "gplots")
new.packages_bioconductor <- list.of.packages_bioconductor[!(list.of.packages_bioconductor %in% installed.packages()[,"Package"])]
new.packages_cran <- list.of.packages_cran[!(list.of.packages_cran %in% installed.packages()[,"Package"])]
# CRAN
if(length(new.packages_cran)>0) install.packages(new.packages_cran)
# Bioconductor
if(length(new.packages_bioconductor)>0) {
source("https://bioconductor.org/biocLite.R")
biocLite(new.packages_bioconductor)
}
Beware that the vignette is rather large and thus takes a minute to compile. You can also see the Vignette at https://shiring.github.io/rna-seq/microarray/2016/09/28/exprAnalysis.
To view the vignette if you built it with the package:
vignette("exprAnalysis", package="exprAnalysis")
vignette("CummeRbund", package="exprAnalysis")
browseVignettes("exprAnalysis")
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