[Bioc-devel] Invalid biocViews terms

[Martin Morgan]

On 09/23/2016 12:15 PM, Martin Morgan wrote:
> Bioc Developers!
>
> biocViews are an important way for users to navigate to your package.
> The following packages have incorrect biocViews terms. To update terms
> in your package, visit
>
>   http://bioconductor.org/packages/devel/BiocViews.html#___Software
>
> check the 'Develoeprs: check this box...' and enter prospective terms in

Developers can also check that box! and also...

> the 'Autocomplete biocViews search' box. Confirm that the term is  under

actually, Autocomplete is user-oriented, and finds terms that at least 
one package uses. So for instance no package has decided to use the 
newly introduced 'SingleCell' term; it's still in the hierarchy under 
Software -> Technology -> SingleCell. And...

> the 'Software' hierarchy. Then update your package in the 'devel'
> branch, remembering to increment the version number (from x.y.z to x.y.z
> + 1).
>
> Terms need to match exactly. They are always CamelCase and never have a
> space or punctuation.

After installing the BiocCheck package,

   R CMD BiocCheck <your-package-source-or-tar.gz>

will validate biocViews terms, and even suggest alternatives.

Martin

>
> Best, Martin
>
>
>
> ADaCGH2 CopyNumberVariants
>
> ASSET Bioinformatics
>
> BaseSpaceR ConnectTools, HighThroughputSequencing
>
> BiGGR Pathway, Systems Biology
>
> bioassayR Bioinformatics
>
> cancerclass Cancer
>
> ccrepe Bioinformatics, Statistics
>
> CGEN MultipleComparisons
>
> ChAMP CopyNumber
>
> chipenrich Bioinformatics, Enrichment
>
> chopsticks SNPsAndGeneticVariability
>
> CNORfeeder Bioinformatics
>
> CNORode Bioinformatics
>
> CNVrd2 Clustering.
>
> cummeRbund Bioinformatics, HighThroughputSequencing,
> HighThroughputSequencingData, MultipleComparisons, RNAseq, RNAseqData
>
> exomePeak HighThroughputSequencing, Methylseq, RNAseq
>
> flowDensity Bioinformatics, Cancer, DensityGating, FlowCytData, StemCells
>
> flowPeaks Gating
>
> GeneAnswers GraphsAndNetworks
>
> globaltest Bioinformatics
>
> iGC Biological Question
>
> isobar Bioinformatics, MultipleComparisons
>
> limma microRNAArray
>
> lmdme Cancer
>
> maSigPro Differential Expression, RNA-Seq
>
> meshr Bioinformatics, MultipleComparisons, Statistics
>
> Metab AMDIS, GCMS
>
> mmnet GraphsAndNetwork
>
> mosaics Bioinformatics, ChIPseq
>
> MPFE HighThroughputSequencingData
>
> nem Bioinformatics, GraphsAndNetworks
>
> networkBMA GraphsAndNetwork
>
> OmicCircos Statistics
>
> plethy Infastructure, biocViews
>
> puma HTA2.0
>
> qcmetrics Bioinformatics, Visualisation
>
> qvalue MultipleComparisons
>
> Rchemcpp Bioinformatics
>
> ReQON HighThroughputSequencing
>
> RMassBank Bioinformatics
>
> roar HighThroughputSequencing, RNAseq
>
> ROntoTools GraphsAndNetworks, NetworkAnalysis
>
> RTN NetworkAnalysis
>
> SamSPECTRAL Cancer, HIV, StemCells
>
> spliceSites RNAseq
>
> sRAP RNAseq, Statistics
>
> supraHex Bioinformatics
>
> VariantFiltering HighThroughputSequencing
>
>
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>
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