The purpose of this pipeline is to streamline the process for analyzing RNA-seq data with potential batch effects.
The pipeline includes:
The functions in this package can be grouped into two main categories:
batchSEQ is the pipeline function. It combines
combatMod into one step.
To begin, install Bioconductor along with a few dependencies that cbcbSEQ uses:
source("http://bioconductor.org/biocLite.R") biocLite(c('limma', 'preprocessCore', 'sva', 'pasilla'))
Next, use devtools to install the latest version of cbcbSEQ from Github:
require(devtools) install_github("cbcbSEQ", user="kokrah")
If all went well you should now be able to load cbcbSEQ:
require(cbcbSEQ) vignette('cbcbSEQIntro', package='cbcbSEQ')
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