README.md

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

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: [e-mail] and [e-mail], many thanks!

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.