biocViews-package: Categorized views of R package repositories

Description

Structures for vocabularies and narratives of views. This can be used to create HTML views of the package structure in a Bioconductor repository.

Arguments

Details

Package:

biocViews

Version:

1.11.4

Depends:

R (>= 2.4.0), methods, utils

Imports:

tools, Biobase, graph (>= 1.9.26), RBGL (>= 1.13.5), XML

Suggests:

Biobase

License:

Artistic-2.0

URL:

http://www.bioconductor.org/packages/release/BiocViews.html

biocViews:

Infrastructure

Index:

BiocView-class          Class "BiocView"
Htmlized-class          Class "Htmlized"
PackageDetail-class     Class "PackageDetail"
RepositoryDetail-class
                        Class "RepositoryDetail"
biocViewsVocab          Bioconductor Task Views Vocabulary Data
extractVignettes        Extract pdf vignettes from local package
                        repository
genReposControlFiles    Generate CRAN-style repository control files
getBiocSubViews         Build a list of BiocView objects from a package
                        repository
getBiocViews            Build a list of BiocView objects from a package
                        repository
getPacksAndViews        Parse VIEWS file for views and packages
getSubTerms             Retrieve a term and its children from a vocab
                        DAG
htmlDoc                 Create a complete HTML document representation
                        of an object
htmlFilename            Return a filename for an object's HTML
                        representation
htmlValue               HTML Representation of an Object
writeBiocViews          Write a list of BiocView objects to HTML
writeHtmlDoc            Write an XML DOM containing HTML to a file
writePackageDetailHtml
                        Write HTML files for packages in a CRAN-style
                        repository
writeRepositoryHtml     Write package descriptions and a repository
                        index as HTML
writeTopLevelView       Write the view for the root of a vocabulary to
                        disk
write_REPOSITORY        Write a REPOSITORY control file for a
                        CRAN-style package repository
write_SYMBOLS           Write a SYMBOLS file
write_VIEWS             Write a VIEWS control file for a CRAN-style
                        package repository

The terms of the vocabulary are stored in a DAG, which can be loaded as the serialized data object biocViewsVocab. For listing of available terms use function getSubTerms.

Further information is available in the following two vignettes:

HOWTO-BCV

Basic package usage

createReposHtml

Further information for repository admins

Examples

Run this code

data(biocViewsVocab)
getSubTerms(biocViewsVocab, "Technology")

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