CLfeats                 produce a data.frame of features relevant to a
                        Cell Ontology class
PROSYM                  PROSYM: HGNC symbol synonyms for PR (protein
                        ontology) entries identified in Cell Ontology
TermSet-class           manage ontological data with tags and a
                        DataFrame instance
allGOterms              allGOterms: data.frame with ids and terms
bind_formal_tags        add mapping from informal to formal cell type
                        tags to a SummarizedExperiment colData
c,TermSet-method        combine TermSet instances
cellTypeToGO            utilities for approximate matching of cell type
                        terms to GO categories and annotations
cleanCLOnames           obtain named character vector of terms from
                        Cell Line Ontology, omitting obsolete and
                        trailing 'cell'
common_classes          list and count samples with common ontological
                        annotation in two SEs
connect_classes         connect ontological categories between related,
                        annotated SummarizedExperiments
ctmarks                 app to review molecular properties of cell
                        types via cell ontology
cyclicSigset            as in Bakken et al. (2017 PMID 29322913) create
                        gene signatures for k cell types, each of which
                        fails to express all but one gene in a set of k
                        genes
demoApp                 demonstrate the use of makeSelectInput
dropStop                dropStop is a utility for removing certain
                        words from text data
fastGrep                some fields of interest are lists, and grep per
                        se should not be used - this function checks
                        and uses grep within vapply when appropriate
findCommonAncestors     Find common ancestors
getCellOnto             load ontologies that may include non-ascii
                        strings and therefore cannot be in data folder
getLeavesFromTerm       obtain childless descendents of a term
                        (including query)
getOnto                 get the ontology based on a short tag and year
humrna                  humrna: a data.frame of SRA metadata related to
                        RNA-seq in humans
improveNodes            inject linefeeds for node names for graph, with
                        textual annotation from ontology
ldfToTerms              use output of cyclicSigset to generate a series
                        of character vectors constituting OBO terms
liberalMap              Produce a data.frame with a set of naive terms
                        mapped to all matching ontology ids and their
                        formal terms
makeSelectInput         generate a selectInput control for an
                        ontologyIndex slice
make_graphNEL_from_ontology_plot
                        obtain graphNEL from ontology_plot instance of
                        ontologyPlot
map2prose               use prose terminology with output of
                        connect_classes
mapOneNaive             use grep or agrep to find a match for a naive
                        token into ontology
minicorpus              minicorpus: a vector of annotation strings
                        found in 'study title' of SRA metadata.
nomenCheckup            repair nomenclature mismatches (to curated term
                        set) in a vector of terms
onto_plot2              high-level use of graph/Rgraphviz for rendering
                        ontology relations
onto_roots              list parentless nodes in ontology_index
                        instance
packDesc2019            packDesc2019: overview of ontoProc resources
packDesc2021            packDesc2021: overview of ontoProc resources
packDesc2022            packDesc2022: overview of ontoProc resources
recognizedPredicates    enumerate ontological relationships used in
                        ontoProc utilities
secLevGen               simple generation of children of 'choices'
                        given as terms, returned as TermSet
selectFromMap           select a set of elements from a term 'map' and
                        return a contribution to a data.frame
seur3kTab               tabulate the basic outcome of PBMC 3K tutorial
                        of Seurat
siblings_TAG            generate a TermSet with siblings of a given
                        term, excluding that term by default
stopWords               stopWords: vector of stop words from xpo6.com
subset_descendants      subset a SummarizedExperiment to which ontology
                        tags have been bound using 'bind_formal_tags',
                        obtaining the 'descendants' of the class of
                        interest
sym2CellOnto            use Cell Ontology and Protein Ontology to
                        identify cell-type defining conditions in which
                        a given gene is named
valid_ontonames         give a vector of valid 'names' of ontoProc
                        ontologies
