[Bioc-devel] New version of rGADEM - ChIP-Seq de novo motif discovery

[Hervé Pagès]

Hi Charles,

On 11-08-05 05:31 AM, Charles Joly wrote:
> Dear all,
>
>
> rGADEM is a de novo motif discovery tool for large scale genomic data that
> is part of an integrated pipeline for ChIP-seq analysis (PICS/rGADEM/MotIV)
> [1]. The program uses openMP in order to greatly reduce some parts of the
> calculation.
>
>
> We are proud to announce a new version of the software, rGADEM 2.0. The code
> is now up-to-date with the latest changes in the GADEM, the c version of the
> program.
>
>
> Notably, two new parameters have been introduced: nmotifs and maskR. With
> nmotifs, it is now possible to stop the analysis once a fixed amount of
> motifs have been found. With the maskR option, low-complexity sequences
> (i.e.: “aaaaaa”, “cacacaca”, etc) are ignored during the analysis.
>
>
> rGADEM is now available in the devel section of bioconductor and should be
> available very soon in the release section.

Thanks for announcing this new version. Someone (Kasper I think) was
pointing recently that Bioconductor doesn't have a tradition of
announcing new package versions even though that's something we've
always encouraged. Yes it could be done more often but that's of course
entirely up to the package authors/maintainers. The only thing we
do systematically is to announce new packages every 6 months at each
new BioC release.

I'd also like to suggest that you do not update the release version of
rGADEM since this really looks like a major update. Packages in BioC
release should not be modified except for minor changes like bug fixes
or documentation improvements.

Thanks,
H.

>
>
> Do not hesitate to contact us directly or through the mailing list if you
> have any questions!
>
>
> Best regards,
>
> Charles Joly Beauparlant.
>
>
> [1] Mercier E., Droit A., Leping L. et al, 2010, An Integrated Pipeline for
> the Genome-Wide Analysis of Transcription Factor Binding Sites from
> ChIP-seq.
>
> 	[[alternative HTML version deleted]]
>
>
>
>
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-- 
Hervé Pagès

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