exprAnalysis

This package implements methods to analyze and visualize expression data.

• It supports normalized input as e.g. from Cufflinks or expression chip arrays and raw count data from bam file input.
• It supports mRNA, miRNA, protein or other expression data.

So far, it is only implemented for human and mouse data!

It uses function from the following packages:

• AnnotationDbi for annotating gene information
• beadarray for importing Illumina expression chip files from GenomeStudio
• clusterProfiler and DOSE for functional enrichment analysis
• DESeq2 for differential expression analysis of raw count data
• GenomicAlignments, GenomicFeatures, Rsamtools for reading bam files
• pcaGoPromoter for principle component analysis
• limma for differential expression analysis of normalised expression data
• pathview for mapping KEGG pathways
• gplots for heatmaps
• sva for batch correction
• WGCNA for coregulatory network determination

Author

Dr. Shirin Glander

Installation

# 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")