(Please cc me on replies, as my mailing list subscription request doesn't seem to have been processed yet.) Hi All, Couple of web site comments: 1) The current layout of the bioconductor.org doesn't provide much guidance to getting started with the bioconductor packages. There is no clear links to documentation and no introduction to the tools. Would it be possible to (at least) give links to the documentation of the individuals packages (not just the function list)? As it is now, it is necessary to download and install the individual packages before having access to the documentation that can be used to see what might really be useful and how the packages interrelate... 2) It is not clear from http://www.bioconductor.org/packages/release/html/index.html what packages are included in the 'Bioconductor Package Bundle' ( Biobase, ROC, annotate, edd, and genefilter), nor is it clear what package are 'required' or 'recommended'. Please list the contents of the 'Bioconductor Package Bundle' as well as adding another column to the individual package listing giving the package 'category'. More complains, suggestions, complements, etc as I get (try to) things working and organized. -Greg LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.

> 1) The current layout of the bioconductor.org doesn't provide much guidance > to getting started with the bioconductor packages. There is no clear links The current layout isn't going to last but a few more weeks, the issues you raise are all being taken into consideration. :) For instance, there will be a full documentation link on the side - as well as links from individual package pages to its vignettes. > 2) It is not clear from > http://www.bioconductor.org/packages/release/html/index.html what packages > are included in the 'Bioconductor Package Bundle' ( Biobase, ROC, > annotate, edd, and genefilter), nor is it clear what package are 'required' > or 'recommended'. Please list the contents of the 'Bioconductor Package Noted. I'm not certain that the package bundle is going to stick around (now that Jianhua's 'getBioC.R' script is available on the site), but if so I'll note this as well. > More complains, suggestions, complements, etc as I get (try to) things > working and organized. Excellent. -Jeff

> -----Original Message----- > From: Jeff Gentry [mailto:jgentry@jimmy.harvard.edu] > Sent: Tuesday, June 18, 2002 10:47 AM > To: Warnes, Gregory R > Cc: 'bioconductor@stat.math.ethz.ch' > Subject: Re: [BioC] Web site suggestions > > > > 1) The current layout of the bioconductor.org doesn't > provide much guidance > > to getting started with the bioconductor packages. There > is no clear links > > The current layout isn't going to last but a few more weeks, > the issues > you raise are all being taken into consideration. :) For > instance, there > will be a full documentation link on the side - as well as links from > individual package pages to its vignettes. Great! That should help a lot. > > > 2) It is not clear from > > > http://www.bioconductor.org/packages/release/html/index.html > what packages > > are included in the 'Bioconductor Package Bundle' ( > Biobase, ROC, > > annotate, edd, and genefilter), nor is it clear what > package are 'required' > > or 'recommended'. Please list the contents of the > 'Bioconductor Package > > Noted. I'm not certain that the package bundle is going to > stick around > (now that Jianhua's 'getBioC.R' script is available on the > site), but if > so I'll note this as well. Unfortunately, the getBioC.R script dies while trying to talk to my http_proxy... More on that in a moment. > > > More complains, suggestions, complements, etc as I get (try > to) things > > working and organized. > > Excellent. > > -Jeff > LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.