Dear Dario
These all look like legitimate suggestions, and probably the package author has
something to say on their substance.
But independent of the specifics here, I think we should also keep in mind that
the motivations for package submission vary across the project.
Some contributors really take it on themselves to continuously develop and
extend a solution for a particular field of science or technology.
This is great, in particular for users.
Others provide a ‘snapshot’ of their work at a particular point in time (e.g.
end of PhD thesis) and make their research reproducible, so that others can
build on top of it. This is the same as with research papers, which are also
rarely supposed to be the “final word” on something but an important advance.
I think this is also great, for the scientific record, and for other method
developers who can start from such a snapshot (if not literally then at least
conceptually) and move on to do even greater things.
Best wishes
Wolfgang
> On Nov 1, 2016, at 6:00 GMT+1, Dario Strbenac <dstr7...@uni.sydney.edu.au>
> wrote:
>
> Hello,
>
> The package FlipFlop is made for isoform quantitiation. Why are there no
> options to specify the RNA-seq read strand ? Otherwise, the method produces
> incorrect counts where overlapping genes on both strands are being
> transcribed. Also, the software requires a SAM file as input. This is
> inefficient, since most mapping results are stored as BAM files. It would be
> better if FlipFlop made more use of the import and export functions available
> in Rsamtools. Also, requiring the gene database to be in BED12 format creates
> more unnecessary work for the user. ENSEMBL and GENCODE both provide GTF and
> GFF3 files, which can easily be imported into R with functions provided by
> rtracklayer.
>
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany
wolfgang.hu...@embl.de
http://www.huber.embl.de
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