Package: biocViews 1.75.0

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:VJ Carey <[email protected]>, BJ Harshfield <[email protected]>, S Falcon <[email protected]> , Sonali Arora, Lori Shepherd <[email protected]>

biocViews_1.75.0.tar.gz
biocViews_1.75.0.zip(r-4.5)biocViews_1.75.0.zip(r-4.4)biocViews_1.75.0.zip(r-4.3)
biocViews_1.75.0.tgz(r-4.4-any)biocViews_1.75.0.tgz(r-4.3-any)
biocViews_1.75.0.tar.gz(r-4.5-noble)biocViews_1.75.0.tar.gz(r-4.4-noble)
biocViews_1.75.0.tgz(r-4.4-emscripten)biocViews_1.75.0.tgz(r-4.3-emscripten)
biocViews.pdf |biocViews.html✨
biocViews/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:biocViews-1.73.1(bioc 3.20)biocViews-1.72.0(bioc 3.19)

infrastructurebioconductor-packagecore-package

9.11 score 4 stars 14 packages 30 scripts 7.0k downloads 32 exports 10 dependencies

Last updated 14 days agofrom:8aa6dafe1f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:coercedump_conceptextractCitationsextractHTMLDocumentsextractManualsextractNEWSextractTopLevelFilesextractVignettesgenReposControlFilesgetBiocSubViewsgetBiocViewsgetCurrentbiocViewsgetPackageNEWSgetSubTermsguessPackageTypehtmlDochtmlFilenamehtmlValueprintNEWSrecommendBiocViewsrecommendPackagesshowvalidate_bioc_viewswrite_REPOSITORYwrite_SYMBOLSwrite_VIEWSwriteBiocViewswriteHtmlDocwritePackageDetailHtmlwriteRepositoryHtmlwriteRFilesFromVignetteswriteTopLevelView

Dependencies:BHBiobaseBiocGenericsBiocManagerbitopsgraphRBGLRCurlRUnitXML

HOWTO generate repository HTML

S. Falcon

Rendered fromcreateReposHtml.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

HOWTO generate biocViews HTML

S. Falcon and V.J. Carey

Rendered fromHOWTO-BCV.Rmdusingknitr::rmarkdownon Oct 30 2024.

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
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