Skip to content
Snippets Groups Projects
Chi Pak's avatar
Update README.md
Chi Pak authored
f78d0ad4
Select Git revision
  • master default
History Find file
Name Last commit Last update
README.md
README.md

Installing R Libraries/Packages

List of R (base) packages that should be installed

  • tidyverse
  • readr
  • parallel
  • Hmisc
  • Rcpp
  • ggpubr
  • viridis
  • MASS
  • knitr

Install them via

module add R/3.3.2-gccmkl_20181025
R
install.packages('tidyverse')
install.packages('readr')
install.packages('parallel')
install.packages('Hmisc')
install.packages('Rcpp')
install.packages('ggpubr')
install.packages('viridis')
install.packages('MASS')
install.packages('knitr')

When you install these packages, it will ask

Would you like to use a personal library instead?  (y/n)

Type y

It will then ask you to select a CRAN mirror

--- Please select a CRAN mirror for use in this session ---
HTTPS CRAN mirror

 1: 0-Cloud [https]                   2: Algeria [https]
 3: Australia (Canberra) [https]      4: Australia (Melbourne 1) [https]
 5: Australia (Melbourne 2) [https]   6: Australia (Perth) [https]
 7: Austria [https]                   8: Belgium (Ghent) [https]
 etc

Look for the USA (TX 1) entry - usually 78

USA (TX 1) [https]

Type the number of this CRAN mirror

To quit out of R

q()
Save workspace image? [y/n/c]:

Type n

List of R Bioconductor packages that should be installed

  • RUVSeq
  • edgeR
  • DESeq2

Install them via

module add R/3.3.2-gccmkl_20181025
R
source("https://bioconductor.org/biocLite.R")
biocLite('RUVSeq')
biocLite('edgeR')
biocLite('DESeq2')