[Bioc-devel] Invalid biocViews terms
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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