Re: [Bioc-devel] IPI numbers in annotation packages

am', I get > > custom_anno/script/bindb.sql > 328:INSERT INTO pfam > > pfam/script/srcdb_pfam.sql > 202:-- INSERT INTO pfamb > > organism_annotation/script/bindb_yeast.sql > 441:-- INSERT INTO pfam > > yeast/script/bindb.sql > 241:-- INSERT INTO pfam > >

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

Works for me. Marc On Tue, Sep 22, 2015 at 6:03 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Marc, > > On 09/22/2015 05:39 PM, Marc Carlson wrote: > >> Herve is right. UCSC doesn't give us this information, And actually, I >> think it's pretty rare to see

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

Herve is right. UCSC doesn't give us this information, And actually, I think it's pretty rare to see exon names from anybody. So it's weird to me that they are a default return value for this method. Marc On Tue, Sep 22, 2015 at 5:29 PM, Hervé Pagès wrote: > Hi

Re: [Bioc-devel] rtracklayer bug?

Hi Arne, So this time when I look at the bioc-devel email list, I don't see a record for this last name (or this email). In fact the only way I could be sure it was you was that your post was the same... ;) If you want to post from gmail, then you will need to subscribe the gmail address to

Re: [Bioc-devel] Changes in AnnotationDbi

) message(message goes here) and they could set pleaseMakeItStop = TRUE in their .Rprofile Is that a reasonable compromise? Jim On Thu, Jun 4, 2015 at 6:06 PM, Marc Carlson mcarl...@fredhutch.org mailto:mcarl...@fredhutch.org wrote: Hi Jim, I do agree that the warning

Re: [Bioc-devel] Changes in AnnotationDbi

Hi Jim, I do agree that the warning was protective for that (this is why I put it there). But it was also annoying for many and a source of some confusion because when people see a warning() they think that something has gone wrong with the code that was just run. And in this case the

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

in the GRanges as mentioned in my previous mail. In the meantime I'll try to fetch the chrom lengths myself but would be nice to have all that ready in the GRanges at some point. cheers, jo On 11 Apr 2015, at 00:54, Marc Carlson mcarl...@fredhutch.org mailto:mcarl...@fredhutch.org wrote: On 04

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

On 04/10/2015 12:18 PM, Rainer Johannes wrote: dear Sonali, Herve, On 10 Apr 2015, at 19:59, Herv� Pag�s hpa...@fredhutch.orgmailto: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

Re: [Bioc-devel] Feature Request--add host and port to makeTxDbPackageFromBiomart

This is done BTW. Marc On 02/27/2015 02:43 PM, Marc Carlson wrote: Hi Sean, This seems like a solid suggestion. I have put it into my queue. Marc On 02/27/2015 04:41 AM, Sean Davis wrote: Hi, Marc. Since Ensembl has switched to GRCh38 for their most recent builds, to get access

Re: [Bioc-devel] keys function of org.Pf.plasmo.db gives an error.

Hi Paolo, The ORF type has never been available for that package. This is a bug in the columns method (which I will now fix). Thanks for reporting it. Marc On 03/18/2015 03:00 AM, Paolo Martini wrote: Dear Bioconductor, I am working with the annotation package org.Pf.plasmo.db. I

Re: [Bioc-devel] keys function of org.Pf.plasmo.db gives an error.

in resources from SGD (which this has nothing to do with since the data all comes from plasmoDB). Anyhow, I have fixed the software bugs and pushed a patch to release and devel. It should be up in about a day. Marc On 03/18/2015 10:23 AM, Marc Carlson wrote: Hi Paolo, The ORF type has never been

Re: [Bioc-devel] Feature Request--add host and port to makeTxDbPackageFromBiomart

Hi Sean, This seems like a solid suggestion. I have put it into my queue. Marc On 02/27/2015 04:41 AM, Sean Davis wrote: Hi, Marc. Since Ensembl has switched to GRCh38 for their most recent builds, to get access to GRCh37 data now requires a different host and port for biomaRt. These are

Re: [Bioc-devel] OrganismDb and associated TxDb

Hi Vince, First of all thank you for using OrganismDb objects. You raise some interesting points though about keeping these APIs better synchronized that I feel point to some deficiencies in the current design. I spoke with Herve about this and we are puzzling over possibly using

Re: [Bioc-devel] Package submission with library requirement

Hi Avinash, So the argument for the importance of reproducible research *definitely* resonates with us here as it is a major goal of ours. However while the decision to use the same library as your paper helps to make the immediate work more reproducible, it simultaneously hampers others

Re: [Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

Hi Peter, I would add that you can see a listing all the currently pre-manufactured TxDb packages here: http://www.bioconductor.org/packages/devel/BiocViews.html#___TxDb And for convenience you can also use an OrgansimDb package to connect the contents of the TxDb package with the older org

Re: [Bioc-devel] FW: GO offspring consistency

Hi Jelle, Thank you for your patience in waiting for my answer here. It took me a lot longer to properly test and validate this than I initially expected. So if you look at amigo you can see these graph views that show you what the current terms up and downstream of a given GO term should

Re: [Bioc-devel] About Hg38 BSgenome

Hi Raffaele, You are in luck today because while we normally do *not* have mechanisms to harmonize the non-standard chromosome names, for this specific case Herve wrote some code to handle it. So you want to look at this: library(GenomeInfoDb) ?fetchExtendedChromInfoFromUCSC Marc On

[Bioc-devel] Google hangout on Wed December 10th for new package authors

Hello new package authors, Based on the number of new software packages being submitted to the project it seems that Bioconductor is more popular than ever. Last release we added a hundred and ten new packages (a new record). A lot of the popularity of this project is because Bioconductor

Re: [Bioc-devel] AnnotationDbi::loadDb() now requires dbType and dbPackage?

Actually they are required in one sense. Just not required of an end user who would be calling the function (so not for that manual page). But they are required in a separate internal sense (which is what the error is referring to) and that is that the database that is loaded it must contain

Re: [Bioc-devel] new error(?) related to annotation: illuminaHumanv1CHR is deprecated

PM, Marc Carlson mcarl...@fhcrc.org mailto:mcarl...@fhcrc.org wrote: Hi Vince, So if you wanted to do this manually, then the thing you would want to do is to get a gene ID from the probe and to take that to a TranscriptDb object (again: that is if you wanted to do

Re: [Bioc-devel] deprecated org.Hs.egCHRLOC UPDATE: the as.list() behaves differently in stable and devel configuration

Hi Raffaele, This problem should be resolved in devel at this time. Please update to the latest version of AnnotationDbi (1.27.14) and try again. Marc On 09/23/2014 02:36 PM, calogero UNITO wrote: affaeleaffaeleHi Vincent, I have further investigated the error I have in the vignette of

Re: [Bioc-devel] new error(?) related to annotation: illuminaHumanv1CHR is deprecated

Hi Vince, So if you wanted to do this manually, then the thing you would want to do is to get a gene ID from the probe and to take that to a TranscriptDb object (again: that is if you wanted to do it manually). Alternatively, if you had an OrganismDb object then this association would be

[Bioc-devel] The release is fast approaching. Information about upcoming deadlines.

Hello package contributors, Please note that next Thursday is the deadline for submitting new packages if you want them to make it into the upcoming October release. You can see the release schedule here: http://www.bioconductor.org/developers/release-schedule/ Please also take note of the

[Bioc-devel] important announcement

Hello, This is a second warning that in less than a week we plan to roll out the new support site for Bioconductor. *Important* Once the support site is 'live', posts to the Bioconductor mailing list will receive an automatic reply indicating that it is no longer in service and directing you to

[Bioc-devel] Announcement about the new support site

Hello, Thank you to those who have participated in the Beta for our new support site. The beta period is now over, and we are getting ready for a formal launch of the site during the week of September 15th. *Important* Once the support site is 'live', posts to the Bioconductor mailing list

Re: [Bioc-devel] Please help us try out our new support site!

watching the mailing list will see relevant questions right away. Stephanie On 8/18/14 12:15 PM, Marc Carlson wrote: Hello! This is a message to announce the beta test for our new support site. We hope to replace the regular Bioconductor mailing list with this site soon and we have imported

[Bioc-devel] Please help us try out our new support site!

Hello! This is a message to announce the beta test for our new support site. We hope to replace the regular Bioconductor mailing list with this site soon and we have imported the past 11+ years of mailing list discussion into this new site. If you would like to help us test it out you can do

Re: [Bioc-devel] Please help us try out our new support site!

and paste (fork) of biostars ( I have nothing against biostars btw) That's my personal opinion of course :) Rad On Aug 18, 2014, at 12:15 PM, Marc Carlson mcarl...@fhcrc.org wrote: Hello! This is a message to announce the beta test for our new support site. We hope to replace the regular

[Bioc-devel] Question about which new organism resources to create

Hi everyone, As many of you already know we have long provided organism annnotation packages that give gene based annotations for selected organisms. And we intend to keep doing that. But these days there is also a lot of other data at NCBI that could be used to make gene based databases

Re: [Bioc-devel] RE : AnnotationDbi and select function

On 03/12/2014 02:53 PM, Marc Carlson wrote: I just checked a fix in for this bug to GenomicFeatures (which happens to be where the problem was). It should percolate out to the build system soon. Marc On 03/12/2014 02:19 PM, Servant Nicolas wrote: Hi guys, Thanks for your feedbacks. Indeed I

Re: [Bioc-devel] Update policy on experiment data and annotation packages

Hi Julian, This is a complicated issue for us and we have to choose our next move carefully since we don't have unlimited resources. Especially not with respect to time. But I wanted to let you know that we appreciate your comment and that we are still thinking about it. Marc On

[Bioc-devel] Courtesy message about the upcoming release

Hello everyone, This is a courtesy message to remind all package developers that next Wednesday the 9th of October is the deadline for all packages to pass the build system without any errors or warnings. Please have a look at our build system for the development branch and make sure that

Re: [Bioc-devel] isActiveSeq deprecated

-friendly on those objects. Thanks, H. On 09/13/2013 10:38 AM, Marc Carlson wrote: Hi Florian, Yes we are trying to make things more uniform. seqlevels() lets you rename as well as deactivate chromosomes you want to ignore, so it was really redundant with isActiveSeq(). So we are moving away from

Re: [Bioc-devel] isActiveSeq deprecated

[13] munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5 [16] RCurl_1.95-4.1 rpart_4.1-3 Rsamtools_1.13.39 [19] RSQLite_0.11.4 rtracklayer_1.21.11 scales_0.2.3 [22] stats4_3.0.1stringr_0.6.2 tools_3.0.1 [25] XML_3.98-1.1zlibbioc_1.7.0 From: Marc Carlson mcarl

Re: [Bioc-devel] isActiveSeq deprecated

Hi Florian, Yes we are trying to make things more uniform. seqlevels() lets you rename as well as deactivate chromosomes you want to ignore, so it was really redundant with isActiveSeq(). So we are moving away from isActiveSeq() just so that users have less to learn about. The reason why

Re: [Bioc-devel] svn for annotation packages

at 1:22 PM, Marc Carlson mcarl...@fhcrc.org mailto:mcarl...@fhcrc.org wrote: Hi Kasper, You should get an email from me in the coming weeks with instructions regarding the upcoming release. If you need something changed before then, please send me an email. Marc

Re: [Bioc-devel] svn for annotation packages

Hi Kasper, You should get an email from me in the coming weeks with instructions regarding the upcoming release. If you need something changed before then, please send me an email. Marc On 09/11/2013 06:17 PM, Dan Tenenbaum wrote: Annotation packages are not in svn. Send your changes

Re: [Bioc-devel] heavy vignette

Hi Carles, In general there are three steps to consider in turn: 1) Look at the repository of experiment data packages. If there are existing packages there with data that you can use then you probably want to use those. 2) Look for ways to make the data smaller and still get your

Re: [Bioc-devel] Fwd: [BioC] Problem reading VCF file using readVcf from package VariantAnnotation

as a result of e.g. a transcripts() or exons() call? Michael On Tue, Apr 30, 2013 at 2:16 PM, Marc Carlson mcarl...@fhcrc.org mailto:mcarl...@fhcrc.org wrote: Related to this: I have added getters for seqinfo (and friends) for the OrganismDb objects. I have not added the setters

[Bioc-devel] Bioconductor and the Google Summer of Code

Hello everyone, This year Bioconductor is participating in the Google Summer of Code. Interested parties can see our GSOC page here: https://google-melange.appspot.com/gsoc/org/google/gsoc2013/bioconductor Also, we know that we only have a few ideas on our ideas list this year. It's because we

[Bioc-devel] Next Wednesday is the deadline for all new package submissions.

Hello everyone, If you are planning to submit a package to the project in time for the upcoming release, please be sure to do so by next Wednesday (the 13th). You can see the deadline in our release schedule here: http://www.bioconductor.org/developers/release-schedule/ Thanks again,

Re: [Bioc-devel] I would like to publish a bioconductor package.

Hi Davide, Lots of good advice here. The main goal with two packages is to minimize dependencies for the experiment data package as this is presumed to be the less specialized package. Whenever you have a package ready please be sure to follow the follow the instructions on the link that

Re: [Bioc-devel] makeTranscriptDBFromGFF v. Flybase GFF

Hi Malcolm, Not too much that hasn't been mentioned before. So I bet that many people can probably walk past this one. Both GFF and GTF files have many of the same things that come up when you use them. They both are being used for things today (like transcriptomes) which represent a

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

Hi Malcolm, In general I have found ensembl to be really great and I expect that their gtf files are probably fine. Usually the exon rank is the 1st thing you will see left out when a gtf file is cutting corners, and you are correct that they seem to be including that. I ran the one for Homo

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

Hi Tengfei, Yes that looks like an oversight. Thanks for reporting that! I will extend makeTxDbPackage so that it's more accommodating of these newer transcriptDbs. If you want to help me out, you could call saveDb() on your gmax189 object and send me the .sqlite file that you save it to.

[Rd] question about assignment warnings for replacement methods

Hi, I have seen several packages that with the most recent version of R are giving a warning like this: Assignments in \usage in documentation object 'marginalData-methods': marginalData(object) = value I assume that this is to prevent people from making assignments in their usage

Re: [Rd] question about assignment warnings for replacement methods

Thank you for the clarifications Duncan. Marc On 04/05/2011 11:15 AM, Duncan Murdoch wrote: On 05/04/2011 1:51 PM, Marc Carlson wrote: Hi, I have seen several packages that with the most recent version of R are giving a warning like this: Assignments in \usage in documentation object