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ivandorsolab
Installing_R_Libraries
Commits
cc7e9daf
Commit
cc7e9daf
authored
6 years ago
by
Chi Pak
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Installing R Libraries/Packages
=====
#### List of R (base) packages that should be installed
*
tidyverse
*
readr
*
parallel
*
Hmisc
*
Rcpp
*
ggpubr
*
viridis
Install them via
```
module add R
R
install.packages('tidyverse')
install.packages('readr')
install.packages('parallel')
install.packages('Hmisc')
install.packages('Rcpp')
install.packages('ggpubr')
install.packages('viridis')
```
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
```
source("https://bioconductor.org/biocLite.R")
biocLite('RUVSeq')
biocLite('edgeR')
biocLite('DESeq2')
```
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