biocViews-package         package:biocViews         R Documentation

_C_a_t_e_g_o_r_i_z_e_d _v_i_e_w_s _o_f _R _p_a_c_k_a_g_e _r_e_p_o_s_i_t_o_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_D_e_t_a_i_l_s:


       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

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>, BJ Harshfield
     <rebjh@channing.harvard.edu>, S Falcon <sfalcon@fhcrc.org>

     Maintainer: Biocore Team c/o BioC user list
     <bioconductor@stat.math.ethz.ch>

_E_x_a_m_p_l_e_s:

     data(biocViewsVocab)
     getSubTerms(biocViewsVocab, "AssayTechnologies")

