Re: [Bioc-devel] Need for file-based handling of meta-data

2016-06-29 Thread Thomas Girke
Great thanks. I will add some ideas later this week or next week. Thomas On Wed, Jun 29, 2016 at 12:44 PM Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 06/29/2016 03:42 PM, Thomas Girke wrote: > > Yes, a "readSummarizedExperiment" would be a "modern-day analog of > > Biobase::readE

Re: [Bioc-devel] Need for file-based handling of meta-data

2016-06-29 Thread Martin Morgan
On 06/29/2016 03:42 PM, Thomas Girke wrote: Yes, a "readSummarizedExperiment" would be a "modern-day analog of Biobase::readExpressionSet". I also agree with the other suggestions including github to get this started, and Vince's thoughts on binding meta-data more tightly to source data as well a

Re: [Bioc-devel] NotNeeded in build report RSS feeds

2016-06-29 Thread Leonardo Collado Torres
Thanks Dan! On Wed, Jun 29, 2016 at 3:54 PM, Dan Tenenbaum wrote: > Indeed, you are right, Leo. I was able to identify the thing that had changed > and to restore it to its previous behavior. It should now behave as before, > only updating the rss feed when the build status has changed. > > Tha

Re: [Bioc-devel] NotNeeded in build report RSS feeds

2016-06-29 Thread Dan Tenenbaum
Indeed, you are right, Leo. I was able to identify the thing that had changed and to restore it to its previous behavior. It should now behave as before, only updating the rss feed when the build status has changed. Thanks, Dan - Original Message - > From: "lcollado" > To: "Antti Honk

Re: [Bioc-devel] Need for file-based handling of meta-data

2016-06-29 Thread Thomas Girke
Yes, a "readSummarizedExperiment" would be a "modern-day analog of Biobase::readExpressionSet". I also agree with the other suggestions including github to get this started, and Vince's thoughts on binding meta-data more tightly to source data as well as improving interoperability. As suggested I

Re: [Bioc-devel] NotNeeded in build report RSS feeds

2016-06-29 Thread Dan Tenenbaum
We didn't (intentionally anyway) change anything with the RSS feeds. We'll look into it. Dan - Original Message - > From: "lcollado" > To: "Antti Honkela" > Cc: "Dan Tenenbaum" , "bioc-devel" > > Sent: Wednesday, June 29, 2016 7:19:26 AM > Subject: Re: [Bioc-devel] NotNeeded in build

Re: [Bioc-devel] NotNeeded in build report RSS feeds

2016-06-29 Thread Dan Tenenbaum
We didn't (intentionally anyway) change anything with the RSS feeds. We'll look into it. Dan - Original Message - > From: "lcollado" > To: "Antti Honkela" > Cc: "Dan Tenenbaum" , "bioc-devel" > > Sent: Wednesday, June 29, 2016 7:19:26 AM > Subject: Re: [Bioc-devel] NotNeeded in build

Re: [Bioc-devel] NotNeeded in build report RSS feeds

2016-06-29 Thread Leonardo Collado Torres
Hi, I don't think this has anything to do with "NotNeeded". The RSS feed did indeed change around the time BioC 3.3 was released and I have also been getting daily RSS updates, even if they are "No build problems for package XYZ" (with the same status the day before). My guess is that the RSS fee

Re: [Bioc-devel] NotNeeded in build report RSS feeds

2016-06-29 Thread Antti Honkela
Hi Dan, I follow the RSS feed on Feedly and for some time now it has shown two updates every day: "NotNeeded in Release" and "NotNeeded in Devel". Up to approximately 2 months ago I only saw updates when the status changed, but since then there have been these two daily non-updates which add

Re: [Bioc-devel] Extending Views to support GRanges (and possibly BigWig files)

2016-06-29 Thread Altuna Akalin
We have this low level functionality in genomation::ScoreMatrixBin (when bin.num=1), where users can give a set of regions they are interested in as GRanges and input data in the form of RleList, GRanges, Bam file or BigWig file, and get the a summary of scores per region of interest. Currently, it