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Question: Outdated packages in R 3.4.2
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gravatar for worldoffred
8 months ago by
worldoffred0 wrote:

Hi all,

New to bioinformatics and am having trouble with RNAseq data analysis - namely alot of the packages recommended are 'not available for R version 3.4.2'
Is there a repository for the most up to date packages of limma and edgeR among others for example?

Thanks in advance

ADD COMMENTlink modified 8 months ago by Gordon Smyth34k • written 8 months ago by worldoffred0
1

Please be more specific. Are you using biocLite from BiocInstaller  1.28.0?

ADD REPLYlink written 8 months ago by Aaron Lun20k
1
gravatar for Gordon Smyth
8 months ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k wrote:

No, there isn't any problem with availability of packages. All the packages used in the limma or edgeR workflows are readily available for R 3.4.2 or 3.4.3. Just follow the installation instructions explained in https://www.bioconductor.org/install .

Briefly you start R, then type

source("https://bioconductor.org/biocLite.R")
biocLite("limma")
biocLite("edgeR")

etc.

This will install the latest versions of the packages.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Gordon Smyth34k
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