[BioC] Votes for biocLite "default" group modifications

Patrick Aboyoun paboyoun at fhcrc.org
Mon Dec 1 21:59:10 CET 2008

BioC Community,
As part of a routine project maintenance effort, we are evaluating the 
packages within "default" group in biocLite to ensure we are adequately 
representing a base installation of Bioconductor. There are currently 29 
packages, plus their dependencies, that are installed when biocLite() is 
called with no arguments:

 > source("http://bioconductor.org/biocLite.R")
 > biocinstallPkgGroups()
 [1] "affy"         "affydata"     "affyPLM"      "annaffy"    
 [5] "annotate"     "Biobase"      "Biostrings"   "DynDoc"     
 [9] "gcrma"        "genefilter"   "geneplotter"  "hgu95av2.db"
[13] "limma"        "marray"       "matchprobes"  "multtest"   
[17] "ROC"          "vsn"          "xtable"       "affyQCReport"
[21] "edd"          "globaltest"   "makecdfenv"   "pamr"       
[25] "siggenes"     "sma"          "statmod"      "tkWidgets"  
[29] "widgetTools"

How well do you think this list refects the core of Bioconductor 
functionality? In order to avoid unnecessary conflict amongst the user 
community, please send me a private e-mail stating which packages you 
believe should be included in and/or removed from the "default" list. In 
a few weeks I will send a follow up email that summarizes our findings. 
In order to guide your responses, you can refer to the package download 
stats located at


Thanks in advance for any assistance you can provide.


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