[Bioc-devel] Extracting mzR compatible acquisition number from mzIdentML files

Hi I'm in the final stage of preparing an mzIdentML parser for submission to Bioconductor (https://github.com/thomasp85/mzID) The parser is intended to be quite sparse and not interpret the content of the mzIdentML file that much. One feature I would like to include though, is that each scan ge

[Bioc-devel] UniProt.ws: Error in .mergeList when mapping to UNIPROTKB

Hi When trying to map from a vector of refseq accessions to uniprot id's I get an error: refseq <- c("YP_139402", "YP_141320", "YP_820357", "YP_006002448", "YP_006040776", "YP_006340074", "YP_006340075", "YP_138830", "YP_819836", "YP_006001858" ) select(UniProt.ws, keys=refseq, keytype="REFSE

[Bioc-devel] Size limits of packages when including other executables

Hi I'm developing a wrapper for the peptide-identification tool MS GF+. The algorithm is developed in Java and the .jar file has a size around 20 mb. For the ease of the user, I think it would make sense to pack the java code together with the wrapper (this has been cleared with the MS GF+ deve

Re: [Bioc-devel] Size limits of packages when including other executables

013 at 1:48 AM, Thomas Dybdal Pedersen > wrote: >> Hi >> >> I'm developing a wrapper for the peptide-identification tool MS GF+. The >> algorithm is developed in Java and the .jar file has a size around 20 mb. >> >> For the ease of the user, I think it

[Bioc-devel] Guidelines for shiny packages

Hi All I’m in the process of getting package submitted to Bioconductor. The package is a pure shiny package and this has led to some - especially one question. For those not familiar with shiny apps, the code that makes these work resides in their own .R files outside of the R directory in a pa

Re: [Bioc-devel] Guidelines for shiny packages

developer to such an extend… best Thomas On 29 Sep 2014, at 21:59, Laurent Gatto wrote: > > On 29 September 2014 20:49, Thomas Dybdal Pedersen wrote: > > Dear Thomas, > >> Hi All >> >> I’m in the process of getting package submitted to Bioconductor. The &

Re: [Bioc-devel] plotPCA for BiocGenerics

While I tend to agree with you that PCA is too big an operation to be hidden within a plotting function (MDS is an edge-case I would say), I can’t see how we can ever reach a point where there is only one generic plot function. In the case of PCA there is a number of different plot-types that ca

Re: [Bioc-devel] Random access to sequences in fasta files

Thanks Martin This was thought as a feauture request/discussion of biostrings, which is why I posted it here. Thought biostrings io capabilities was behind most other fasts readers on bioconductor... /Thomas > Den 29/01/2015 kl. 15.45 skrev Martin Morgan : > >> On 01/29/2015 06:41 AM, Thomas

Re: [Bioc-devel] BiocCheck required import

Sure, sorry. Its available on GitHub at thomasp85/FindMyFriends > Den 03/09/2015 kl. 16.57 skrev Dan Tenenbaum : > > > > - Original Message - >> From: "Dan Tenenbaum" >> To: "Thomas Lin Pedersen" >> Cc: bioc-devel@r-project.org >> Sent: Thursday, September 3, 2015 7:55:42 AM >> Subjec