[BioC] supraHex for tabular omics data analysis using a supra-hexagonal map

Steve Lianoglou lianoglou.steve at gene.com
Wed Nov 6 15:57:31 CET 2013


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

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

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

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.



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]]
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Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology

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