MiRComb R package
There are two ways of installing miRComb from GitHub:
Use devtools package:
library(devtools)
if(!require(miRData)) install_github("mariavica/miRData", ref="master", build_vignettes = TRUE)
install_github("mariavica/miRComb", ref="master", build_vignettes = TRUE)(use build_vignettes = FALSE if you have problems with vignettes intallation)
Or with githubinstall package:
library(githubinstall)
if(!require(miRData)) gh_install_packages("miRData", ref = "master", build_vignettes = TRUE)
gh_install_packages("miRComb", ref = "master", build_vignettes = TRUE)In both cases, use ref="patch-devel" if you want to install the latest version.
Otherwise, you can also download the source files from sourceforge.net: https://sourceforge.net/projects/mircomb/files/?source=navbar
Other R/Bioconductor packages are needed, if you want to install all of them, type:
install.packages(c("gplots","gtools","network","WriteXLS","Hmisc","glmnet","scatterplot3d", "VennDiagram","xtable","survival","pheatmap","mvoutlier","mclust"))
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("RankProd","clusterProfiler","limma","KEGG.db","circlize","ReactomePA","DESeq","DO.db")) Use and comments
If the package has been useful for you, we will be very grateful if you can cite our article:
- Vila-Casadesús M, Gironella M, Lozano JJ (2016) MiRComb: An R Package to Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers. PLoS ONE 11(3): e0151127. doi:10.1371/journal.pone.0151127
Also, feel free to make comments or suggestions in this GitHub Repository or to: maria.vila.bioinfo@gmail.com and juanjo.lozano@ciberehd.org, many thanks!