[Bioc-sig-seq] News about PICS/rGADEM/MotIV

[Droit Arnaud]

Hi All,

We just wanted to send you a news update about PICS, rGADEM and MotIV. As you may already know, all three packages are now available from Bioconductor.
You can now go from short reads to enriched regions, validated motifs, motifs occurrences, and modules using our pipeline. We have worked very hard to make it as easy as possible to use.
Our packages are well integrated with other Bioconductor packages (IRanges, ChIPpeakAnno, Rsamtools....) which makes it easy for users to construct sophisticated analysis approaches that also leverage other R/Bioconductor functionally

We are still improving the overall pipeline and we would love to hear from you if you have any comments/suggestions that could improve it further.

Please note that we have fixed a bug in PICS preventing the proper normalization of the enrichment scores. Among other things this could have affected the proper estimation of the FDR so we recommend you to upgrade to version 1.01 (Release 1.2.0). In addition, release 1.2.0 now supports the multicore package and improve some of the graphics capabilities. The default is to use multicore over snowfall, so if both packages are loaded, multicore will be used and the number of cores will automatically be set for you based on your machine. We have included a NEWS file in PICS, so type news(package="PICS") for details.

Similarly, rGADEM (as of 1.0.0) also include supports for multicore based calculation via Grand Central Dispatch and this is only available on snow leopard. No special configuration is required as long as you are running snow leopard on a multicore machine rGADEM will use multiple cores. Although GCD is also available on FreeBSD, it's not yet available on other *nix systems, so we will look at openmp as on option. We will keep you posted as soon as we have a working version. The multicore version of rGADEM is way faster!

MotIV (1.1.3) has also been updated so that now jaspar motifs and scores are automatically exported and don't need to be loaded.

Finally, we are working in developing tutorials that will be complementary to the vignettes provided. These will be available on our wiki: wiki.rglab.org. Preliminary tutorials for PICS and rGADEM are already available.
Again comments/suggestions are welcome.

Arnaud.

Bioinformatician/Programmer Analyst
Computational Biology Research Unit
Clinical Research Institute of Montreal (IRCM)
110, avenue des Pins Ouest
Montréal (Québec) H2W 1R7
url: http://www.rglab.org