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README
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README
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###################################################
#### README for miRComb and miRData packages ####
###################################################
I. Package installation -----------------------
I.a. Linux/Mac users --------------------
Download miRComb and miRData to your local folder. Into R session, type:
install.packages("miRData_x.x.tar.gz")
install.packages("miRComb_x.x.tar.gz")
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","mvoutiler","mclust",
"pROC","mvoutlier"))
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("RankProd","clusterProfiler","limma","circlize","ReactomePA","DESeq",
"GO.db"))
I.b. Windows users ------------------
MiRComb and miRData packages can be downloaded here to your local folder:
http://sourceforge.net/projects/mircomb/files/WindowsVersions/
Into R session type:
install.packages("miRData_x.x.zip")
install.packages("miRComb_x.x.zip")
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","mvoutiler","mclust",
"pROC","mvoutlier"))
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("RankProd","GOstats","limma","RamiGO","circlize","ReactomePA","DESeq",
"GO.db"))
II. Use --------
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
III. Comments / problems ------------------------
If you have any other question/problem regarding to installation, or you
have further comments don't hesitate to write us (maria.vila@ciberehd.org):
we will try to answer as soon as possible.
Many thanks and enjoy the software!