[Bioc-devel] Updating biocViews of your package

Nishant Gopalakrishnan ngopalak at fhcrc.org
Thu Mar 19 23:39:52 CET 2009

Hi Keith

Thanks a lot for bringing that inconsistency up to our attention.

The biocViews were recently updated with the following changes.

1. The section Statistics was renamed to Bioinformatics.
2. The section Computational Domains was renamed to Infrastructure.
3. Preprocessing and Quality control were brought under Bioinformatics
4. Multichannel was added under the section AssayTechnologies-> Microarray

Patrick has updated the description files of all packages that had the
Statistics BiocViews term to Bioinformatics.

The link  http://wiki.fhcrc.org/bioc/biocViews_categories  now displays
the correct information for the limma package.



Keith Satterley wrote:
> Hi Nishant,
> Whilst checking my affylmGUI and limmaGUI packages, I noticed that
> there is an inconsistency in the BiocViews page at:
> http://wiki.fhcrc.org/bioc/biocViews_categories
> and the list of BiocView categories at:
> http://bioconductor.org/packages/devel/biocViews/index.php
> You have used the BiocViews entry from the limma package DESCRIPTION
> file as an example. In particular:
> biocViews: Microarray, OneChannel, TwoChannel, DataImport,
> QualityControl, Preprocessing, Statistics, DifferentialExpression,
> MultipleComparisons, TimeCourse
> It includes the term "Statistics". However from my viewing of the list
> of terms on the index page mentioned above, there is not a Statistics
> term.
> Should there still be a Statistics term in BiocViews (as there used to
> be)?
> Gordon doesn't have a problem in changing his limma DESCRIPTION file
> if that's what you would like,
> cheers,
> Keith
> ========================
> Keith Satterley
> Bioinformatics Division
> The Walter and Eliza Hall Institute of Medical Research
> Parkville, Melbourne,
> Victoria, Australia
> =======================
> Nishant Gopalakrishnan wrote:
>> Dear Bioconductor developers,
>> We have been reviewing the cataloging of Bioconductor packages to ensure
>> that new users can easily identify packages that meet their
>> requirements. biocViews is a categorization system that helps users
>> navigate the growing collection of packages in Bioconductor. The
>> biocViews field in the DESCRIPTION file of each package determines the
>> views under which each package appears in.
>> The Bioconductor task views can be found at
>> http://bioconductor.org/packages/release/BiocViews.html
>> The views provided by biocViews integrate the software, annotation data
>> and experiment data repositories provided by Bioconductor, thereby
>> helping users identify packages that best suit their requirements.
>> With the Bioconductor 2.3 release, we have updated the list of biocViews
>> terms.
>> The updated list can be found at
>> http://bioconductor.org/packages/devel/biocViews/index.php
>> With the upcoming release of Bioconductor 2.4, we would like to
>> encourage use of appropriate biocViews. We request all package
>> maintainers to update their package DESCRIPTION files with updated
>> biocViews terms most appropriate for their package.
>> If you have additional questions, please contact us by posting to the
>> bioc-devel mailing list.  We will be glad to help.
>> Thanks in advance for your time and effort,
>> The Bioconductor core team
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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