[BioC] new package for generating interactive HTML reports

[Sean Davis]

On Fri, Jan 11, 2013 at 10:19 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> The package is extensible to the point that you could simply create a new
> type of report that is output as some wiki language, so it wouldn't be
> necessary to fork or modify ReportingTools. If there are internal utilities
> for generating data tables that might be usefully shared, they could be
> exposed, or at least factored out for ":::" access.

There are also tools like the ascii package that can output various R
data types (including data.frames) in various formats
(markdown/pandoc, asciidoc, rst, org, textile, txt2tags).

Sean


> On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro <xavier.depedro at vhir.org>wrote:
>
>> 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<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<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/<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
>>
>>
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