Package: ontoProc
Title: processing of ontologies of anatomy, cell lines, and so on
Authors@R: c(person(given="Vincent", family="Carey", role=c("ctb", "cre"),
	   email = "stvjc@channing.harvard.edu",
           comment = c(ORCID = "0000-0003-4046-0063")),
	     person(given="Sara", family="Stankiewicz", role="ctb",
	     email = "reshs@channing.harvard.edu"), person(given="Victor", family="Tarca", role="ctb", 
		email = "vtarca11@gmail.com", comment = c(ORCID = "0009-0003-1976-0392")))
Description: Support harvesting of diverse bioinformatic ontologies,
        making particular use of the ontologyIndex package on CRAN. We
        provide snapshots of key ontologies for terms about cells, cell
        lines, chemical compounds, and anatomy, to help analyze
        genome-scale experiments, particularly cell x compound screens.
        Another purpose is to strengthen development of compelling use
        cases for richer interfaces to emerging ontologies.
Version: 2.7.0
Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache,
        shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT,
        igraph, AnnotationHub, SummarizedExperiment, reticulate,
        R.utils, httr, basilisk, jsonlite, RBGL, ellmer
Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle,
        SingleCellExperiment, celldex, rmarkdown, AnnotationDbi,
        magick,
Depends: R (>= 4.1), ontologyIndex
License: Artistic-2.0
LazyLoad: yes
biocViews: Infrastructure, GO
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Encoding: UTF-8
Collate: 'CLextend.R' 'CLfeats.R' 'autism_details.R'
        'available_ontos.R' 'basilisk.R' 'bind_formal_tags.R'
        'bioregistry.R' 'clfixer.R' 'common_classes.R'
        'connect_classes.R' 'countClasses.R' 'ctmarks.R' 'data.R'
        'dropStop.R' 'fastGrep.R' 'findCommonAncestors.R' 'formalize.R'
        'getOntos.R' 'get_ordo_owl_path.R' 'graphNEL.R' 'mapNaive.R'
        'nio_details.R' 'ontoDiff.R' 'owl2cache.R' 'owl_ops.R'
        'plot.owlents.R' 'quickOnto.R' 'roots.R' 'setup_entities2.R'
        'seurTab.R' 'shiny.R' 'subset_descendants.R' 'sym2CellOnto.R'
        'termProc.R' 'treeproc.R'
URL: https://github.com/vjcitn/ontoProc
BugReports: https://github.com/vjcitn/ontoProc/issues
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 18:29:37 UTC
RemoteUrl: https://github.com/bioc/ontoProc
RemoteRef: HEAD
RemoteSha: 9f24f7924ba42392967929c5117c531b67c4fe4c
NeedsCompilation: no
Packaged: 2026-07-04 19:05:39 UTC; root
Author: Vincent Carey [ctb, cre] (ORCID:
    <https://orcid.org/0000-0003-4046-0063>),
  Sara Stankiewicz [ctb],
  Victor Tarca [ctb] (ORCID: <https://orcid.org/0009-0003-1976-0392>)
Maintainer: Vincent Carey <stvjc@channing.harvard.edu>