Package: biocViews 1.81.0

Bioconductor Package Maintainer

biocViews: Categorized views of R package repositories

Infrastructure to support 'views' used to classify Bioconductor 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.

Authors:Vincent Carey [aut], Benjamin Harshfield [aut], Seth Falcon [aut], Sonali Arora [aut], Lori Shepherd [aut], Bioconductor Package Maintainer [cre]

biocViews_1.81.0.tar.gz
biocViews_1.81.0.zip(r-4.7)biocViews_1.81.0.zip(r-4.6)biocViews_1.81.0.zip(r-4.5)
biocViews_1.81.0.tgz(r-4.6-any)biocViews_1.81.0.tgz(r-4.5-any)
biocViews_1.81.0.tar.gz(r-4.7-any)biocViews_1.81.0.tar.gz(r-4.6-any)
biocViews_1.81.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
biocViews/json (API)

# Install 'biocViews' in R:
install.packages('biocViews', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/biocviews/issues

Datasets:

On BioConductor:biocViews-1.81.0(bioc 3.24)biocViews-1.80.0(bioc 3.23)

infrastructurebioconductor-packagecore-package

9.49 score 4 stars 15 packages 45 scripts 4 mentions 35 exports 11 dependencies

Last updated from:472ce5b9e9. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR174
linux-devel-x86_64NOTE181
source / vignettesOK237
linux-release-x86_64NOTE211
macos-release-arm64NOTE123
macos-oldrel-arm64NOTE143
windows-develNOTE116
windows-releaseNOTE119
windows-oldrelNOTE110
wasm-releaseOK172

Exports:build_db_from_sourcebuild_meta_aliases_dbbuild_meta_rdxrefs_dbcoercedump_conceptextractCitationsextractHTMLDocumentsextractManualsextractNEWSextractTopLevelFilesextractVignettesgenReposControlFilesgetBiocSubViewsgetBiocViewsgetCurrentbiocViewsgetPackageNEWSgetSubTermsguessPackageTypehtmlDochtmlFilenamehtmlValueprintNEWSrecommendBiocViewsrecommendPackagesshowvalidate_bioc_viewswrite_REPOSITORYwrite_SYMBOLSwrite_VIEWSwriteBiocViewswriteHtmlDocwritePackageDetailHtmlwriteRepositoryHtmlwriteRFilesFromVignetteswriteTopLevelView

Dependencies:BHBiobaseBiocGenericsBiocManagerbitopsgenericsgraphRBGLRCurlRUnitXML

HOWTO generate biocViews HTML
Overview | Establishing a vocabulary of terms | Use Case: adding a term to the vocabulary | Use Case: updating BioConductor website | Querying a repository | Generating HTML
Rendered fromHOWTO-BCV.Rmdusingknitr::rmarkdown

Last update: 2022-08-03
Started: 2022-08-03

HOWTO generate repository HTML
Overview | CRAN-style Layout | Extracting vignettes | Generating the control files | Generating the HTML | Design and extension notes | Details on HTML generation | A note on the htmlValue method for PackageDetail
Rendered fromcreateReposHtml.Rmdusingknitr::rmarkdown

Last update: 2022-08-03
Started: 2022-08-03

Readme and manuals

Help Manual

Help pageTopics
Categorized views of R package repositoriesbiocViews-package biocViews
Class "BiocView"BiocView-class bvPackageTable-class bvParentViews-class bvSubViews-class bvTitle-class coerce,BiocView,rdPackageTable-method htmlDoc,BiocView-method htmlFilename,BiocView-method htmlValue,BiocView-method htmlValue,bvParentViews-method htmlValue,bvSubViews-method show,BiocView-method
Bioconductor Task Views Vocabulary DatabiocViewsVocab
Helper functions to generate HTML pages for reference manualsbuild-dbs build_db_from_source build_meta_aliases_db build_meta_rdxrefs_db
produce character stream for use with Protege entities/class hierarchy ingestion based on biocViews subgraphsdump_concept
Extract Rd man pages and build pdf reference manuals from local package repositoryextractCitations extractManuals
Extract NEWS files from source package tarballsextractNEWS
Extract files from the top level of source package tarballsextractTopLevelFiles
Extract pdf vignettes from local package repositoryextractHTMLDocuments extractVignettes
Generate CRAN-style repository control filesgenReposControlFiles
Build a list of BiocView objects from a package repositorygetBiocSubViews
Build a list of BiocView objects from a package repositorygetBiocViews
Get a list of biocViews for each branchgetCurrentbiocViews
Retrieve and print package NEWSgetPackageNEWS printNEWS
Retrieve list of package titles and print package DescriptiongetPackageDescriptions getPackageTitles
Parse VIEWS file for views and packagesgetPacksAndViews makeVocInfo permulist pump tellSubTop tellSuperTop
Retrieve a term and its children from a vocab DAGgetSubTerms
Guess Package Type (Software, ExperimentData, AnnotationData) using existing biocViews.guessPackageType
Create a complete HTML document representation of an objecthtmlDoc
Return a filename for an object's HTML representationhtmlFilename htmlFilename,character-method
Class "Htmlized"htmlDoc,Htmlized-method Htmlized-class
HTML Representation of an ObjecthtmlValue
Class "PackageDetail"htmlDoc,PackageDetail-method htmlFilename,PackageDetail-method htmlValue,PackageDetail-method htmlValue,pdAuthorMaintainerInfo-method htmlValue,pdDescriptionInfo-method htmlValue,pdDetailsInfo-method htmlValue,pdDownloadInfo-method htmlValue,pdVignetteInfo-method htmlValue,pdVigsAndDownloads-method PackageDetail-class pdAuthorMaintainerInfo-class pdDescriptionInfo-class pdDetailsInfo-class pdDownloadInfo-class pdVignetteInfo-class pdVigsAndDownloads-class
Recommend biocViews for an existing Package.recommendBiocViews
Recommend Packages using existing biocViews.recommendPackages
Class "RepositoryDetail"htmlDoc,RepositoryDetail-method htmlFilename,RepositoryDetail-method htmlValue,rdPackageTable-method htmlValue,RepositoryDetail-method rdPackageTable-class RepositoryDetail-class
Validate a package's biocViews.validate_bioc_views validation_tests
Write a REPOSITORY control file for a CRAN-style package repositorywrite_REPOSITORY
Write a SYMBOLS filewrite_SYMBOLS
Write a VIEWS control file for a CRAN-style package repositorywrite_VIEWS
Write a list of BiocView objects to HTMLwriteBiocViews
Write an XML DOM containing HTML to a filewriteHtmlDoc
Write HTML files for packages in a CRAN-style repositorywritePackageDetailHtml
Write package descriptions and a repository index as HTMLwriteRepositoryHtml
Write R files from vignetteswriteRFilesFromVignettes
Write the view for the root of a vocabulary to diskwriteTopLevelView