| allGOterms | allGOterms: data.frame with ids and terms |
| ancestors | retrieve ancestor 'sets' |
| ancestors_names | obtain list of names of a set of ancestors |
| bind_formal_tags | add mapping from informal to formal cell type tags to a... |
| cellTypeToGO | utilities for approximate matching of cell type terms to GO... |
| children_names | obtain list of names of a set of subclasses/children |
| cleanCLOnames | obtain named character vector of terms from Cell Line... |
| CLfeats | produce a data.frame of features relevant to a Cell Ontology... |
| common_classes | list and count samples with common ontological annotation in... |
| connect_classes | connect ontological categories between related, annotated... |
| c-TermSet-method | combine TermSet instances |
| ctmarks | app to review molecular properties of cell types via cell... |
| cyclicSigset | as in Bakken et al. (2017 PMID 29322913) create gene... |
| demoApp | demonstrate the use of makeSelectInput |
| dropStop | dropStop is a utility for removing certain words from text... |
| fastGrep | some fields of interest are lists, and grep per se should not... |
| findCommonAncestors | Find common ancestors |
| getCellOnto | basic getters in old style, retained 2023 for deprecation... |
| get_classes | return a generator with ontology classes |
| getLeavesFromTerm | obtain childless descendents of a term (including query) |
| getOnto | get the ontology based on a short tag and year |
| get_ordo_owl_path | decompress ordo owl file |
| humrna | humrna: a data.frame of SRA metadata related to RNA-seq in... |
| improveNodes | inject linefeeds for node names for graph, with textual... |
| labels.owlents | retrieve labels with names |
| ldfToTerms | use output of cyclicSigset to generate a series of character... |
| liberalMap | Produce a data.frame with a set of naive terms mapped to all... |
| make_graphNEL_from_ontology_plot | obtain graphNEL from ontology_plot instance of ontologyPlot |
| makeSelectInput | generate a selectInput control for an ontologyIndex slice |
| map2prose | use prose terminology with output of connect_classes |
| mapOneNaive | use grep or agrep to find a match for a naive token into... |
| minicorpus | minicorpus: a vector of annotation strings found in 'study... |
| nomenCheckup | repair nomenclature mismatches (to curated term set) in a... |
| onto_plot2 | high-level use of graph/Rgraphviz for rendering ontology... |
| onto_roots | list parentless nodes in ontology_index instance |
| owl2cache | cache an owl file accessible via URL |
| packDesc2019 | packDesc2019: overview of ontoProc resources |
| packDesc2021 | packDesc2021: overview of ontoProc resources |
| packDesc2022 | packDesc2022: overview of ontoProc resources |
| packDesc2023 | packDesc2023: overview of ontoProc resources |
| parents | retrieve is_a |
| plot.owlents | visualize ontology selection via onto_plot2, based on owlents |
| print.owlents | short printer |
| PROSYM | PROSYM: HGNC symbol synonyms for PR (protein ontology)... |
| recognizedPredicates | enumerate ontological relationships used in ontoProc... |
| secLevGen | simple generation of children of 'choices' given as terms,... |
| selectFromMap | select a set of elements from a term 'map' and return a... |
| setup_entities | construct owlents instance from an owl file |
| seur3kTab | tabulate the basic outcome of PBMC 3K tutorial of Seurat |
| siblings_TAG | generate a TermSet with siblings of a given term, excluding... |
| stopWords | stopWords: vector of stop words from xpo6.com |
| subclasses | retrieve subclass entities |
| sub-.owlents | subset method |
| subset_descendants | subset a SummarizedExperiment to which ontology tags have... |
| sym2CellOnto | use Cell Ontology and Protein Ontology to identify cell-type... |
| TermSet-class | manage ontological data with tags and a DataFrame instance |
| url_ok | check that a URL can get a 200 for a HEAD request |
| valid_ontonames | give a vector of valid 'names' of ontoProc ontologies |
