A fast R implementation using Rcpp based on the original matlab HCP method for Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge by Mostafavi et al. PLOSone (2013).
From unix and alike use either:
library(devtools)
install_github("mvaniterson/Rhcpp")Or using the biocLite function from BioConductor:
source("http://bioconductor.org/biocLite.R")
biocLite("mvaniterson/Rhcpp")see ?hcp or the unitTest directory for examples. The package contains example data from the original paper.