The BiocInstaller package
library(BiocInstaller)
defines appropriate repositories biocinstallRepos() that can be queried for
available packages that are named consistently with your needs
nms = row.names(available.packages(contrib.url(biocinstallRepos())))
want = grep("Hsapiens|Mmusculus", nms, value=TRUE)
(there are about 30 of these; maybe you don't want them all?) and retrieved
using biocLite
biocLite(want)
It might also be interesting to identify relevant AnnotationHub resources,
e.g., in devel
library(AnnotationHub)
hub = AnnotationHub()
and query (in devel; in release you would use metadata(hub) and search through
that) to discover the 5339 relevant resources
> query(hub, "sapiens")
class: AnnotationHub
length: 5339
filters: none
hubUrl: http://annotationhub.bioconductor.org/ah
snapshotVersion: 3.0/1.5.3; snapshotDate: 2014-04-01
hubCache: /home/mtmorgan/.AnnotationHub
Martin
----- Dario Strbenac <dstr7...@uni.sydney.edu.au> wrote:
> Hello,
>
> I would like to install all software packages and also all annotation
> packages containing the pattern Hsapiens or Mmusculus in their name. I know
> about biocLite(all_group()) to do the first task, but I'm not sure if it's
> possible to query the repository with a pattern. The installation guide
> simply advises "Visit the Workflows page and software package list to
> discover available packages."
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
