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| 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-method | combine TermSet instances |
| cellTypeToGenes | utilities for approximate matching of cell type terms to GO categories and annotations |
| cellTypeToGO | utilities for approximate matching of cell type terms to GO categories and annotations |
| children_TAG | generate a TermSet with siblings of a given term, excluding that term by default |
| cleanCLOnames | obtain named character vector of terms from Cell Line Ontology, omitting obsolete and trailing 'cell' |
| CLfeats | produce a data.frame of features relevant to a Cell Ontology class |
| 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 |
| getCellLineOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getCellOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getCellosaurusOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getChebiLite | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getChebiOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getDiseaseOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getEFOOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getGeneOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getHCAOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getLeavesFromTerm | obtain childless descendents of a term (including query) |
| getMondoOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getOncotreeOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getPATOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getPROnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getSIOOnto | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| getUBERON_NE | load ontologies that may include non-ascii strings and therefore cannot be in data folder |
| 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 |
| label_TAG | generate a TermSet with siblings of a given term, excluding that term by default |
| 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 |
| PROSYM | PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology |
| 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 |
| show | manage ontological data with tags and a DataFrame instance |
| show-method | manage ontological data with tags and a DataFrame instance |
| 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 |
| TermSet-class | manage ontological data with tags and a DataFrame instance |