Dear Users and Developers, This short email is to notify our new package called 'supraHex' that is intended to analyse and visualise any tabular omics data. The supraHex is able to carray out gene clustering/meta-clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. More importantly, it allows for overlaying additional data to explore relations between input and additional data. To bring its benefits to the widest audiences, in addition to the User Manual we have also prepared a dedicated webpage ( http://supfam.org/SUPERFAMILY/dcGO/supraHex.html), from which you can easily get started. Best Wishes, Hai Fang, Dr. Bioinformatics Research Associate, Computational Genomics Group, Depart of Computer Science University of Bristol, UK [[alternative HTML version deleted]]

Hello, I just checked out your web page to see what this package does, but before reading through your vignette I ran into a rather large red flag. Your installation instructions for using the "strongly recommended" development version will likely be a source of pain for people who follow your instructions (and to those of us who need to help them dig themselves out of a hole when they complain about version problems on this list :-). Your website includes a strong suggestion for users to install the development version by switching BiocInstaller to "devel" mode (ie. useDevel=TRUE) and install your package that way, but that will then ask to convert/upgrade the user's entire bioconductor ecosystem over to the development version, which is not what most users should be doing. Perhaps you could rather provide instructions to your users on how to download the development version of your package via SVN and install the package from the command line. Or, better/easier yet, put your package up on github and let people install it via devtools::install_github. Whatever you end up doing, please don't encourage people to switch on the BiocInstaller::useDevel() function, as the unaware user will end up in a whole world of hurt since they will be running software that was not intended to be released just yet. Thanks, -steve On Tue, Nov 5, 2013 at 4:09 AM, Hai Fang <hfang.shanghai at="" gmail.com=""> wrote: > Dear Users and Developers, > > This short email is to notify our new package called 'supraHex' that is > intended to analyse and visualise any tabular omics data. The supraHex is > able to carray out gene clustering/meta-clustering and sample correlation, > plus intuitive visualisations to facilitate exploratory analysis. More > importantly, it allows for overlaying additional data to explore relations > between input and additional data. > > To bring its benefits to the widest audiences, in addition to the User > Manual we have also prepared a dedicated webpage ( > http://supfam.org/SUPERFAMILY/dcGO/supraHex.html), from which you can > easily get started. > > > Best Wishes, > > Hai Fang, Dr. > Bioinformatics Research Associate, > Computational Genomics Group, > Depart of Computer Science > University of Bristol, UK > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech