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: 2.3.11
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
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: 8aa7338
git_last_commit_date: 2025-10-08
Repository: Bioconductor 3.22
Date/Publication: 2025-10-09
NeedsCompilation: no
Packaged: 2025-10-09 23:17:59 UTC; biocbuild
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>
