biocViews: Categorized views of R package repositories

Infrastructure to support Bioconductor 'views' used to classify software packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'experiment data' packages.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("biocViews")
AuthorVJ Carey <stvjc@channing.harvard.edu>, BJ Harshfield <rebjh@channing.harvard.edu>, S Falcon <sfalcon@fhcrc.org> , Sonali Arora
Bioconductor views Infrastructure
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.44.0
http://www.bioconductor.org/packages/release/BiocViews.html

View on Bioconductor

Man pages

BiocView-class: Class "BiocView"

biocViews-package: Categorized views of R package repositories

biocViewsVocab: Bioconductor Task Views Vocabulary Data

extractManuals: Extract Rd man pages and build pdf reference manuals from...

extractNEWS: Extract NEWS files from source package tarballs

extractTopLevelFiles: Extract files from the top level of source package tarballs

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

getCurrentbiocViews: Get a list of biocViews for each branch

getPackageNEWS: Retrieve and print package NEWS

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

Htmlized-class: Class "Htmlized"

htmlValue: HTML Representation of an Object

PackageDetail-class: Class "PackageDetail"

recommendBiocViews: Recommend biocViews for an existing Package.

recommendPackages: Recommend Packages using existing biocViews.

RepositoryDetail-class: Class "RepositoryDetail"

validation_tests: Validate a package's biocViews.

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

write_REPOSITORY: Write a REPOSITORY control file for a CRAN-style package...

writeRepositoryHtml: Write package descriptions and a repository index as HTML

writeRFilesFromVignettes: Write R files from vignettes

write_SYMBOLS: Write a SYMBOLS file

writeTopLevelView: Write the view for the root of a vocabulary to disk

write_VIEWS: Write a VIEWS control file for a CRAN-style package...

Functions

BiocView-class Man page
biocViews Man page
biocViews-package Man page
biocViewsVocab Man page
bvPackageTable-class Man page
bvParentViews-class Man page
bvSubViews-class Man page
bvTitle-class Man page
coerce,BiocView,rdPackageTable-method Man page
extractCitations Man page
extractHTMLDocuments Man page
extractManuals Man page
extractNEWS Man page
extractTopLevelFiles Man page
extractVignettes Man page
genReposControlFiles Man page
getBiocSubViews Man page
getBiocViews Man page
getCurrentbiocViews Man page
getPackageNEWS Man page
getPacksAndViews Man page
getSubTerms Man page
htmlDoc Man page
htmlDoc,BiocView-method Man page
htmlDoc,Htmlized-method Man page
htmlDoc,PackageDetail-method Man page
htmlDoc,RepositoryDetail-method Man page
htmlFilename Man page
htmlFilename,BiocView-method Man page
htmlFilename,character-method Man page
htmlFilename,PackageDetail-method Man page
htmlFilename,RepositoryDetail-method Man page
Htmlized-class Man page
htmlValue Man page
htmlValue,BiocView-method Man page
htmlValue,bvParentViews-method Man page
htmlValue,bvSubViews-method Man page
htmlValue,PackageDetail-method Man page
htmlValue,pdAuthorMaintainerInfo-method Man page
htmlValue,pdDescriptionInfo-method Man page
htmlValue,pdDetailsInfo-method Man page
htmlValue,pdDownloadInfo-method Man page
htmlValue,pdVignetteInfo-method Man page
htmlValue,pdVigsAndDownloads-method Man page
htmlValue,rdPackageTable-method Man page
htmlValue,RepositoryDetail-method Man page
makeVocInfo Man page
PackageDetail-class Man page
pdAuthorMaintainerInfo-class Man page
pdDescriptionInfo-class Man page
pdDetailsInfo-class Man page
pdDownloadInfo-class Man page
pdVignetteInfo-class Man page
pdVigsAndDownloads-class Man page
permulist Man page
printNEWS Man page
pump Man page
rdPackageTable-class Man page
recommendBiocViews Man page
recommendPackages Man page
RepositoryDetail-class Man page
show,BiocView-method Man page
tellSubTop Man page
tellSuperTop Man page
validate_bioc_views Man page
validation_tests Man page
writeBiocViews Man page
writeHtmlDoc Man page
writePackageDetailHtml Man page
write_REPOSITORY Man page
writeRepositoryHtml Man page
writeRFilesFromVignettes Man page
write_SYMBOLS Man page
writeTopLevelView Man page
write_VIEWS Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/as-methods.R R/getPackNames.R R/getPackageNEWS.R R/htmlDoc-methods.R R/htmlFilename-methods.R R/htmlValue-methods.R R/packageDetails.R R/pump.R R/recommendBiocViews.R R/repository.R R/show-methods.R R/showvoc.R R/validation_tests.R
build
build/vignette.rds
data
data/biocViewsVocab.rda
inst
inst/css
inst/css/package-detail.css.in
inst/css/repository-detail.css.in
inst/doc
inst/doc/HOWTO-BCV.R
inst/doc/HOWTO-BCV.Rnw
inst/doc/HOWTO-BCV.pdf
inst/doc/VIEWS
inst/doc/createReposHtml.R
inst/doc/createReposHtml.Rnw
inst/doc/createReposHtml.pdf
inst/dot
inst/dot/biocViewsVocab.dot
inst/extdata
inst/extdata/biocViewsVocab.sqlite
inst/htmlfrags
inst/htmlfrags/topfrag.html
inst/script
inst/script/recommend_biocViews_rpacks.R inst/script/reviseBiocViews.R inst/script/revise_expt_biocViews.R inst/script/revisebiocViews2014.R
inst/unitTests
inst/unitTests/CITATION-tmpl
inst/unitTests/test_biocViews.R inst/unitTests/test_citations.R
man
man/BiocView-class.Rd man/Htmlized-class.Rd man/PackageDetail-class.Rd man/RepositoryDetail-class.Rd man/biocViews-package.Rd man/biocViewsVocab.Rd man/extractManuals.Rd man/extractNEWS.Rd man/extractTopLevelFiles.Rd man/extractVignettes.Rd man/genReposControlFiles.Rd man/getBiocSubViews.Rd man/getBiocViews.Rd man/getCurrentbiocViews.Rd man/getPackageNEWS.Rd man/getPacksAndViews.Rd man/getSubTerms.Rd man/htmlDoc.Rd man/htmlFilename.Rd man/htmlValue.Rd man/recommendBiocViews.Rd man/recommendPackages.Rd man/validation_tests.Rd man/writeBiocViews.Rd man/writeHtmlDoc.Rd man/writePackageDetailHtml.Rd man/writeRFilesFromVignettes.Rd man/writeRepositoryHtml.Rd man/writeTopLevelView.Rd man/write_REPOSITORY.Rd man/write_SYMBOLS.Rd man/write_VIEWS.Rd
tests
tests/runTests.R
updateVocab.sh
vignettes
vignettes/HOWTO-BCV.Rnw
vignettes/createReposHtml.Rnw

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