Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

this over the weekend. Thomas On Thu, Oct 22, 2015 at 5:39 PM Arora, Sonali <sar...@fredhutch.org> wrote: Hi Thomas, I get the following error when I try to obtain the feature types using the function genFeatures() library(systemPipeR) library(GenomicFeatures) Loading required p

Re: [Bioc-devel] New biocView - RiboSeq

Hi Thomas, Thanks for tagging your package with RiboSeq - Sorry about missing systemPipeR in my last email. Sonali. On 10/20/2015 4:34 PM, Arora, Sonali wrote: Recently a new biocView called 'RiboSeq' was added to the list of biocViews to tag packages working with Ribsome Profiling

[Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

Hi Thomas, I get the following error when I try to obtain the feature types using the function genFeatures() > library(systemPipeR) > library(GenomicFeatures) Loading required package: AnnotationDbi > txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene") Download the refGene

[Bioc-devel] New biocView - RiboSeq

Recently a new biocView called 'RiboSeq' was added to the list of biocViews to tag packages working with Ribsome Profiling Sequence Data. http://www.bioconductor.org/packages/devel/BiocViews.html and then navigates to Software -> Technology -> Sequencing -> RiboSeq (this is __without__ the

[Bioc-devel] Documentation Section of Package Landing Page messed up

Hi, I checked this with three browsers on my machine ( Chrome, Firefox and IE) If a package has multiple vignettes on its package landing page, All the links for the vignettes are collapsed and displayed next to only one of them. This is happening in both devel and release. For an example,

Re: [Bioc-devel] Documentation Section of Package Landing Page messed up

Thanks for the quick fix, Dan ! Sonali. On 10/19/2015 2:24 PM, Dan Tenenbaum wrote: Hi Sonali, - Original Message - From: "Sonali Arora" To: "bioc-devel" Sent: Monday, October 19, 2015 12:32:45 PM Subject: [Bioc-devel] Documentation

[Bioc-devel] Error in GenomicFeatures::makeTxDbFromUCSC()

Hi , I get an error when creating a txdb object for hg19 from the refGene Table > txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene") Error in tableNames(ucscTableQuery(session, track = track)) : error in evaluating the argument 'object' in selecting a method for function

Re: [Bioc-devel] Bug Report - for goseq - for RefSeq Genes track - RefSeq identifiers or Entrez Gene ID ?

. Cheers, Nadia. On 10 Oct 2015, at 8:15 am, Arora, Sonali <sar...@fredhutch.org> wrote: Hi everyone, I am using goseq to perform Gene Ontology analysis of RNA-seq data and I think I found the following bug. Since my RNA-seq data was aligned using Refseq table - so I need to sup

[Bioc-devel] Bug Report - for goseq - for RefSeq Genes track - RefSeq identifiers or Entrez Gene ID ?

Hi everyone, I am using goseq to perform Gene Ontology analysis of RNA-seq data and I think I found the following bug. Since my RNA-seq data was aligned using Refseq table - so I need to supply id as "refGene" which are actually EntrezId's from goseq::supportedGeneIDs() The bug is - that

Re: [Bioc-devel] Txdb Issues - all exon names are NA's ?

9_group=genes_track=knownGene_table=knownGene_doSchema=describe+table+schema > > The exon information is all coming from the exonStarts and exonEnds > columns. No exon names! > > H. > > PS: Maybe this would better be asked on the support site. > > &

[Bioc-devel] Txdb Issues - all exon names are NA's ?

Hi everyone, I was trying to get the exons by gene from a txdb object but I get NA's for all exon_name's. Please advise. > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > ebg2 <- exonsBy(txdb, by="gene") > > ebg2 GRangesList object of length 23459: $1

[Bioc-devel] new biocView ExperimentData -ReproducibleResearch

Hi everyone, We have added a new biocView ExperimentData - ReproducibleResearch http://bioconductor.org/packages/devel/BiocViews.html#___ReproducibleResearch This biocView is tagged with experiment data packages which contain reproducible results and data from a journal publication/book.

Re: [Bioc-devel] triform - Bioconductor Package up for Adoption

:49 AM, Arora, Sonali wrote: Dear Bioconductor Deevlopers, The current developers of triform are no longer be able to maintain this package, thus, triform is now up for adoption. http://bioconductor.org/packages/triform One can read more about the package : http://bioconductor.org/packages

Re: [Bioc-devel] AnnotationHubData Error: Access denied: 530

...@fredhutch.org mailto:hpa...@fredhutch.org wrote: Hi Johannes, Sonali, On 04/10/2015 09:40 AM, Arora, Sonali wrote: Hi Rainer, Just to be clear - what do you want to be available from AnnotationHub() in the end? Currently the GTF files from Ensembl are already present inside the AnnotationHub

[Bioc-devel] Reminder: Deadline for new package submissions - March 27, 2015

Hi everyone, Just a reminder - Friday, March 27, 2015 is the deadline for submitting new packages. If you submit your package on Friday, your package will still be considered for the upcoming release. A detailed release schedule can be found here:

[Bioc-devel] Deadline for new package submissions - March 27, 2015

Hello everyone, Please note that Thursday, March 27, 2015 is the deadline for submitting new packages if you want them to make it into the upcoming April 2015 release. You can see the full release schedule at: http://www.bioconductor.org/developers/release-schedule/ Thanks and Regards,

[Bioc-devel] New biocViews for devel branch.

Hello everyone, The new and revised biocViews suggested by us are now live. Link to previously suggested biocViews email: (https://stat.ethz.ch/pipermail/bioc-devel/2014-February/005257.html) We have made the following changes: 1. Modified all the packages in devel (2.14) to reflect the latest

Re: [Bioc-devel] Revising biocViews

. On 2/20/2014 12:31 PM, Arora, Sonali wrote: Hello everyone, We have been working to revise the biocViews. We are suggesting changes only to the software branch. Please see the attached document suggestedbiocViews.pdf for the suggested changes. To see the suggested biocView tree structure

[Bioc-devel] Revising biocViews

Hello everyone, We have been working to revise the biocViews. We are suggesting changes only to the software branch. Please see the attached document suggestedbiocViews.pdf for the suggested changes. To see the suggested biocView tree structure , please look at:

Re: [Bioc-devel] Revising biocViews

Attaching the document - suggestedbiocViews.pdf Thanks and Regards, Sonali Arora On 2/20/2014 12:31 PM, Arora, Sonali wrote: Hello everyone, We have been working to revise the biocViews. We are suggesting changes only to the software branch. Please see the attached document

Re: [Bioc-devel] request: high-level seqlevel utilities

, one could then extract using keepSeqlevels() #as shown earlier: keepSeqlevels(got,c(chrX,chrY)) keepSeqlevels(got,c(chrX,chrY, chrM)) Thanks and Regards Sonali. On 12/25/2013 4:15 AM, Michael Lawrence wrote: Awesome -- how about keepAutosomes? On Tue, Dec 24, 2013 at 1:11 PM, Arora, Sonali

Re: [Bioc-devel] request: high-level seqlevel utilities

GenomicRanges depend on AnnotationDbi. That's a major change. Before, it was just in Suggests. Did you discuss this with anyone? Michael On Fri, Dec 27, 2013 at 11:37 AM, Arora, Sonali sar...@fhcrc.org mailto:sar...@fhcrc.org wrote: Hi Michael, We decided to come up with one

Re: [Bioc-devel] request: high-level seqlevel utilities

Hi Michael, That is an extremely interesting question. We have a couple of ideas and are beginning to work on it. We hope to come up with something soon. Thanks, Sonali. On 12/16/2013 6:14 AM, Michael Lawrence wrote: should be stored with the Seqinfo. It could be imputed (along with the