[Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

Mon Dec 7 22:13:34 CET 2015

Thanks,

I've changed it to
biocViews: Software, DataImport, DataRepresentation, Preprocessing

Cheers,

Marcin

2015-12-02 22:52 GMT+01:00 Hervé Pagès <hpages at fredhutch.org>:

> Hi Marcin,
>
> BTW I noticed that RTCGA has no biocViews (only Software). Populating
> the biocViews field with appropriate and specific terms will make
> your packages show up in the corresponding views here
>
>   http://bioconductor.org/packages/release/BiocViews.html#___Software
>
> and thus will greatly improve the chances that the user in the need
> of functionalities like the ones you provide will discover your package.
>
> Cheers,
> H.
>
>
> On 11/22/2015 10:39 AM, Morgan, Martin wrote:
>
>> Marcin -- I join with Herve in strongly discouraging you from this
>> approach. Because you wish only to change upper versus lower case of your
>> package name, and because some operating systems ignore case, your package
>> will go through a release where it is not available under either upper- or
>> lower-case variant. This will confuse and alienate your users, even more
>> than changing the package name to something completely different. There are
>> a number of packages, including some of our own, where the name could have
>> been chosen more carefully, but we have learned to live with our changes of
>> mind. After all, you can still claim to be consistent with the naming
>> convention of the RTCGA.clinical and RTCGA.mutations package ;)
>>
>> I guess Dario was referring to
>>
>>    library(AnnotationHub)
>>    hub = AnnotationHub()
>>    eset = query(hub, "GSE62944")[[1]]
>>
>> with
>>
>> eset
>>>
>> ExpressionSet (storageMode: lockedEnvironment)
>> assayData: 23368 features, 7706 samples
>>    element names: exprs
>> protocolData: none
>> phenoData
>>    sampleNames: TCGA-02-0047-01A-01R-1849-01
>>      TCGA-02-0055-01A-01R-1849-01 ... TCGA-ZG-A8QZ-01A-11R-A37L-07 (7706
>>      total)
>>    varLabels: bcr_patient_barcode bcr_patient_uuid ... CancerType (421
>>      total)
>>    varMetadata: labelDescription
>> featureData: none
>> experimentData: use 'experimentData(object)'
>> Annotation:
>>
>>> table(eset$CancerType)
>>>
>>
>> BLCA BRCA COAD  GBM HNSC KICH KIRC KIRP LAML  LGG LIHC LUAD LUSC   OV
>> PRAD READ
>>   273 1082  468  170  481   66  540  226  164  528  212  514  490  344
>> 423  164
>> SKCM STAD THCA UCEC
>>   373  146  506  536
>>
>>> print(object.size(eset), units="auto")
>>>
>> 264.5 Mb
>>
>>> ov = eset[, eset$CancerType == "OV"]   ## ovarian samples
>>>
>>
>> The data are Rsubread summarized counts from before the May update. In
>> the near term, we are actively expanding offerings derived from that GSE to
>> include the May update; this is in conjunction with efforts to develop an
>> 'ExperimentHub' analog of AnnotationHub, for more experiment-centric,
>> heavily curated resources.
>>
>> It is a little unclear whether the AnnotationHub and your data are
>> redundant or complementary, and whether they can be combined into a single
>> offering. One philosophical difference is the use of semantically rich and
>> integrated ExpressionSet versus basic data structures (data.frame, in your
>> case). We also differ in when we separate data into cancer types; we opted
>> for the entire data set because it is not impossibly large. And our data
>> are AnnotationHub-based rather than package-based. Obviously, avoiding
>> redundant access to the same data is beneficial. One possibility is to
>> collaboratively curate the data into AnnotationHub / ExperimentHub
>> resources, and to tailor access via packages that reference the resource
>> (e.g., one can retrieve the GRASP2 data base through AnnotationHub as
>> resource AH21414, or via grasp2db::GRASP2(); the latter comes with
>> documentation for manipulating the resource).
>>
>> It seems like there are similar opportunities for collaboration and
>> reduced redundancy between the RTCGA, RTCGAToolbox, and TCGAbiolinks
>> packages.
>>
>> Martin Morgan
>> Bioconductor
>>
>> ________________________________________
>> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Marcin
>> Kosiński [m.p.kosinski at gmail.com]
>> Sent: Sunday, November 22, 2015 11:37 AM
>> To: Dario Strbenac
>> Cc: bioc-devel at r-project.org
>> Subject: Re: [Bioc-devel] Is there a way to change the name of R package
>> that is already published on bioconductor?
>>
>> Hi Herve,
>>
>> I think I would like to proceed with such technical possibility.
>> I'd like to keep consistency with the RTCGA.miRNASeq package that I am
>> uploading to bioconductor with issue 1335.
>> Can we schedule such operation?
>>
>> Best,
>> Marcin
>>
>>
>>
>> Hi Dario,
>>
>> Do you want to tell me that there is a possibility to load RNASeq datasets
>> for all available 38 cancer types/cohorts from the last release date
>> (21-08-2015) of datasets from The Cancer Genome Atlas with the use of
>> AnnotationHub?
>>
>> Is it as simple as:
>>
>> library(AnnotationHub)
>> BRCA.RNASeq -> x
>>
>> ?
>>
>> Best,
>> Marcin
>>
>> 2015-11-17 0:00 GMT+01:00 Dario Strbenac <dstr7320 at uni.sydney.edu.au>:
>>
>> Hello,
>>>
>>> How does your package differ to importing GSE62944 into R with
>>> AnnotationHub
>>> http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It
>>> seems like unnecessary duplication.
>>>
>>> --------------------------------------
>>> Dario Strbenac
>>> PhD Student
>>> University of Sydney
>>> Camperdown NSW 2050
>>> Australia
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
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> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
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> Seattle, WA 98109-1024
>
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>

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