biocViews-package: Categorized views of R package repositories

In biocViews: 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.

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

Author(s)

VJ Carey <[e-mail]>, BJ Harshfield <[e-mail]>, S Falcon <[e-mail]>

Maintainer: Biocore Team c/o BioC user list <[e-mail]>

Examples

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

biocViews documentation built on Nov. 19, 2020, 2:01 a.m.