Re: [Bioc-devel] Updating CausalR package after igraph fix

Hi Glyn, It looks like CausalR is broken in release and devel. You'll need to make the changes to both branches - check out, make changes, bump the version and check in. Complete instructions are here: http://bioconductor.org/developers/how-to/source-control/ New functions should be added to

[Bioc-devel] Updating CausalR package after igraph fix

Hi All, Our package CausalR depends on igraph and so broke when igraph was updated last year. We have now fixed CausalR to work with the latest igraph, but we're not sure how we need to go about updating it on Bioconductor, - can we just submit our fixed package as an update, or do we need to

Re: [Bioc-devel] mcols<-() behaviour inheriting from Vector vs GRanges

Fantastic, thanks Herve. On Tue, Jan 5, 2016 at 1:32 AM, Hervé Pagès wrote: > This is fixed in S4Vectors release (0.8.6) and devel (0.9.16). > > Cheers, > H. > > > On 01/04/2016 11:52 AM, Hervé Pagès wrote: > >> Hi Malcolm, >> >> Thanks for reporting this. Will fix. >> >>

[Bioc-devel] Bioconductor Newsletter: January 2016

http://www.bioconductor.org/help/newsletters/2016_January/ Happy New Year! Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the

[Bioc-devel] Creating Biostrings DNAStringSet from Rcpp/C++

Forgive the really naive questions, but my C/C++ and Biostrings skills are pretty rough. I have been playing with Rcpp to interface to an external library for reading sequence formats. I am reading DNA sequences one-at-a-time and would like to package a set of those up as a DNAStringSet. I

Re: [Bioc-devel] Creating Biostrings DNAStringSet from Rcpp/C++

You're going to want to use the Biostrings C API. You can see TwoBitFile_read() in src/twoBit.c in rtracklayer for an example. It's not trivial. Michael On Tue, Jan 5, 2016 at 5:21 AM, Sean Davis wrote: > Forgive the really naive questions, but my C/C++ and Biostrings

Re: [Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

On Jan 5, 2016 7:01 PM, "Tim Triche, Jr." wrote: > > 1) this is a support.bioconductor.org question > 2) don't use .db0 packages, you will rue the day you did Can you expand on this statement? Right now all of the ChipDb are built using a db0 package, so it's not clear to

[Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

Hello, Happy new year. What is the common work-flow to build an microarray annotation package, like hgu133a.db. For some array, there are probe sequences available, then maybe mapping is used? While for other situations, how to deal with? If code used by the team available, that will be great.

Re: [Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

1) this is a support.bioconductor.org question 2) don't use .db0 packages, you will rue the day you did best, --t On Tue, Jan 5, 2016 at 3:53 PM, Zhilong Jia wrote: > Hello, > > Happy new year. > > What is the common work-flow to build an microarray annotation package, >