Question: Where is DEXSeq bioconductor package?
0
gravatar for Fabrice Tourre
8.4 years ago by
Fabrice Tourre970 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.ht ml Thanks.
dexseq • 704 views
ADD COMMENTlink modified 8.4 years ago by Simon Anders3.6k • written 8.4 years ago by Fabrice Tourre970
Answer: Where is DEXSeq bioconductor package?
0
gravatar for Sean Davis
8.4 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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
ADD COMMENTlink written 8.4 years ago by Sean Davis21k
On Sat, Jul 23, 2011 at 5:04 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > 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. Fixed. Sorry for the inconvenience. > 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 >
ADD REPLYlink written 8.4 years ago by Sean Davis21k
It works. Thanks. On Sun, Jul 24, 2011 at 12:01 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Sat, Jul 23, 2011 at 5:04 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> 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/DEXSe q.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. > > Fixed. ?Sorry for the inconvenience. > >> 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 >> >
ADD REPLYlink written 8.4 years ago by Fabrice Tourre970
Answer: Where is DEXSeq bioconductor package?
0
gravatar for SimonNoël
8.4 years ago by
SimonNoël450
SimonNoël450 wrote:
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
ADD COMMENTlink written 8.4 years ago by SimonNoël450
Answer: Where is DEXSeq bioconductor package?
0
gravatar for SimonNoël
8.4 years ago by
SimonNoël450
SimonNoël450 wrote:
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
ADD COMMENTlink written 8.4 years ago by SimonNoël450
Answer: Where is DEXSeq bioconductor package?
0
gravatar for Simon Anders
8.4 years ago by
Simon Anders3.6k
Zentrum für Molekularbiologie, Universität Heidelberg
Simon Anders3.6k wrote:
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
ADD COMMENTlink written 8.4 years ago by Simon Anders3.6k
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