readme.md

In rmflight/ccPaper: work for categoryCompare paper revisions

ccPaper

This is the work for all the analysis in the categoryCompare publication and make it easier to work with. To allow testing and incorporation of new features for the reviewers and readers, a specific branch of the categoryCompare Bioconductor package now exists in the public repository based on the most recent Bioconductor release.

Supplementary Results / Data

If you are just looking for the supplementary results / data, they are available as web-pages for this site.

• Hypothetical Example
• CROHNS vs UC
• Skin vs Muscle Denervation

In addition, they are also provided as package vignettes as part of the ccPaper package. For access to the data and scripts underlying the reported results, follow the instructions below to install the ccPaper package.

categoryCompare Paper Branch Installation

source("http://bioconductor.org/biocLite.R")
library(BiocInstaller)
biocLite(c("KEGG.db", "GO.db", "categoryCompare")) # install current bioconductor version
install_github("categoryCompare", username="rmflight", ref="paper", quick=TRUE) # install the version for ccPaper

Note that the quick=TRUE part is required if running an up-to-date version of devtools.

This will install the package categoryComparePaper, thus named so that it does not change any other version of categoryCompare previously installed. Note that the categoryComparePaper package should be installed prior to installing this package, as this one depends on it.

ccPaper Installation

library(devtools)
library(BiocInstaller)
biocLite(c("ALL", "hgu95av.db", "hgu133plus2.db", "limma")) # other required packages
library(devtools)
install_github("ccPaper", "rmflight", quick=TRUE) # install this package

rmflight/ccPaper documentation built on May 27, 2019, 9:31 a.m.