Dear list, Here is a introduce to DEXSeq. It is a bioconductor package. But I can not find where to download it. http://rna-seqblog.com/data-analysis/expression-tools/dexseq- inference-of-differential-expression-and-splicing-in-rna-seq/ And the link provided in the blog does not work. http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.ht ml Thanks.

On Sat, Jul 23, 2011 at 10:34 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: > Dear list, > > Here is a introduce to DEXSeq. It is a bioconductor package. But I can > not find where to download it. > > http://rna-seqblog.com/data-analysis/expression-tools/dexseq- inference-of-differential-expression-and-splicing-in-rna-seq/ > > And the link provided in the blog does not work. > > http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq. html My bad. I run the Bioconductor mirror mentioned in the blog and misconfigured one of the scripts I use to maintain the mirror. The link should be working again in a couple of hours. In the meantime, you can use the main bioconductor site. Note that DEXSeq is available only in the development archive, so you will need to be running the development version of R in order to use DEXSeq. Sean

Hi, I can't really help.. But there strange thing there... With google cache, you can see a download like that look incorect : source("http:///biocLite.R") Usualy, there are only 2 /. The adresse I use when I need package is source("http://bioconductor.org/biocLite.R"). Also, the information say it's for development version 2.9 of bioconductor... So maby it's in a part of it's development where it's not usable... So maby a developer can help. I am only using version 2.8... Theysay that the author are Simon Anders and Alejandro Reyes , both at EMBL Heidelberg. Theyalso say that the maintainer is Alejandro Reyes. You should try to contact them as your next step. Simon No?l CdeC ________________________________________ De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Fabrice Tourre [fabrice.ciup at gmail.com] Date d'envoi : 23 juillet 2011 12:34 ? : Bioconductor mailing list Objet : [BioC] Where is DEXSeq bioconductor package? Dearlist, Hereis a introduce to DEXSeq. It is a bioconductor package. But I can not find where to download it. http://rna-seqblog.com/data-analysis/expression-tools/dexseq- inference-of-differential-expression-and-splicing-in-rna-seq/ And the link provided in the blog does not work. http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.ht ml Thanks. _______________________________________________ Bioconductormailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Searchthe archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

I have take a look at the dev section. You can see that your package is at http://bioconductor.org/packages/2.9/bioc/html/DEXSeq.html You can also see that they are error for that package http://bioconductor.org/checkResults/2.9/bioc-LATEST/ Package 127/483 Hostname OS / Arch BUILD CHECK BUILD BIN DEXSeq 0.1.12 Alejandro Reyes Last Changed Rev: 56770 / Revision: 56895 Last Changed Date: 2011-07-15 14:22:18 -0700 wilson2 Linux (openSUSE 11.4) / x86_64 OK OK liverpool Windows Server 2003 R2 (32-bit) / x64 OK ERROR OK gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64 OK ERROR OK moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64 OK ERROR OK pitt Mac OS X Leopard (10.5.8) / i386 OK OK OK Package 128/483 Hostname OS / Arch BUILD CHECK BUILD BIN But I don't know the exact meaning of those error because I am not a dev and haven't read ther guide. Simon No?l CdeC ________________________________________ De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Fabrice Tourre [fabrice.ciup at gmail.com] Date d'envoi : 23 juillet 2011 12:34 ? : Bioconductor mailing list Objet : [BioC] Where is DEXSeq bioconductor package? Dear list, Here is a introduce to DEXSeq. It is a bioconductor package. But I can not find where to download it. http://rna-seqblog.com/data-analysis/expression-tools/dexseq- inference-of-differential-expression-and-splicing-in-rna-seq/ And the link provided in the blog does not work. http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.ht ml Thanks. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Just to clarify: As indicated by the fact that it is available in the devel branch only and not in release branch, DEXSeq is not yet released, and it has not yet gone through the official Bioconductor peer review process required for inclusion in the release. DEXSeq is more or less finished even though we are still busy with some polishing and testing. If you want to try out the current beta version, go ahead, but please be aware that there might still be a few rough corners. Any feed-back is most welcome, of course. Simon