[BioC] new package for generating interactive HTML reports

[Xavier de Pedro]

Dear Josh & co.:

Thanks for producing such a package, it looks promising indeed!

I see that it uses jquery data tables, and the live filtering of the 
data is very fast (nice!).
I have a few quick questions, after a quick review of your vignette and 
examples:

Have you experienced any issues when the data set contained in the 
browser is very large (regardless that you set the browser to display 
just 10 records at a time; I understand that the whole data set is 
loaded in the browser)?

And in my relaxed todo list (without hurries) I had the idea to create a 
similar package to produce wiki syntax for tables from R data frames, 
and to display png (or svg) images within pages to be displayed through 
wiki engines (with it's appropriated syntax for the wiki engine of 
interest). A few years ago I had to do that and I produced some custom 
function 'ad hoc' without releasing it (yet) in any R package. In our 
example, we run r scripts through Tiki (wiki) pages, through PluginR, 
but the output is either bare text (so far) or images (png or svg), and 
any modification is handled by R commands by hand. And a function to 
produce the "Fancy Tables" that Tiki can produce with "JQuery Sortable 
Tables" is needed ( http://doc.tiki.org/PluginFancyTable ). I foresee 
that maybe the datatable jquery plugin could be even better for that, 
since it contains pagination and live filtering, which can be very very 
handy!.

And maybe you are open to receive improvements/extensions to your 
package to support other ways to produce the tables required for better 
integration for wiki engines such as Tiki? Or should I fork from your 
package?

Thanks in advanced, and congratulations for the generic package that you 
created.

Xavier

On 11/01/13 00:49, Josh Kaminker wrote:
> Hi all,
>
> We present a new R package,
> ReportingTools<http://www.bioconductor.org/packages/devel/bioc/html/ReportingTools.html>,
> for transforming the output of various Bioconductor packages into
> interactive web pages.  We have found this package very useful in our
> collaborations with both bench and other computational scientists.  Examples
> and instructions for generating output using this package can be found
> here: http://research-pub.gene.com/ReportingTools/
>
> With just three lines of user code, rich HTML documents can be generated
> from the result objects produced by several standard Bioconductor packages
> including edgeR, limma, GOstats, and GSEAlm.  By default, ReportingTools
> reports include hyperlinks to relevant external databases and are highly
> interactive through the use of filtering and sorting options provided by
> open source javascript libraries.  Supporting javascript and css libraries
> are included with all reports, allowing them to be examined on a local
> computer without a network connection.  Additionally, in-line graphics have
> been developed to accompany statistical results to allow convenient visual
> inspection of underlying raw data.  ReportingTools output is highly
> customizable and this package can be used equally well to share results
> from automated pipeline processes or individual customized analyses.
>
> We are very interested in receiving your feedback including feature
> requests for this package.
>
> Best regards,
>
> Josh Kaminker
> Melanie Huntley
> Jason Hackney
> Jessica Larson
> Christina Chaivorapol
>
>


-- 
Xavier de Pedro Puente, Ph.D.
Statistics and Bioinformatics Unit (UEB)
High Technology Unit (UAT)
Vall d'Hebron Research Institute (VHIR). Mediterranean Building
Passeig de la Vall d'Hebron, 119-129
08035 Barcelona. Catalonia. Spain
  
Ph. +34 934894007 / Fax +34 934894015
xavier.depedro at vhir.org
http://ueb.vhir.org