[BioC] Votes for biocLite "default" group modifications

[Patrick Aboyoun]

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

http://bioconductor.org/packages/stats

Thanks in advance for any assistance you can provide.


Patrick