| allGOterms |
allGOterms: data.frame with ids and terms |
| ancestors |
retrieve ancestor 'sets' |
| ancestors_names |
obtain list of names of a set of ancestors |
| available_ontos |
interrogate the cache for owl files and serialized ontologyIndex instances |
| bind_formal_tags |
add mapping from informal to formal cell type tags to a SummarizedExperiment colData |
| bioregistry_ols_resources |
produce bioregistry_ols table |
| browse_ontos |
browse available ontologies with datatable |
| 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_names |
obtain list of names of a set of subclasses/children |
| 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 |
| formalize |
use an LLM to match informal terms to terms in an ontology |
| getCellosaurusOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getChebiLite |
basic getters in old style, retained 2023 for deprecation interval |
| getChebiOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getDiseaseOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getGeneOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getHCAOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getLeavesFromTerm |
obtain childless descendents of a term (including query) |
| getMondoOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getOncotreeOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getOnto |
get the ontology based on a short tag and year |
| getPATOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getPROnto |
basic getters in old style, retained 2023 for deprecation interval |
| getSIOOnto |
basic getters in old style, retained 2023 for deprecation interval |
| getUBERON_NE |
basic getters in old style, retained 2023 for deprecation interval |
| get_classes |
return a generator with ontology classes |
| get_ordo_owl_path |
decompress ordo owl file |
| graph2paths |
produce list of vectors of (shortest) paths from root to all nodes in gr |
| 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 |
| jowl2classgraph |
extract class relationship graph from JSON representation of OWL |
| jowl2classgraph_nio |
extract class relationship graph from JSON representation of OWL for NIO |
| labels.owlents |
retrieve labels with names |
| 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 |
| ontoDiff |
Display Version Differences |
| onto_plot2 |
high-level use of graph/Rgraphviz for rendering ontology relations |
| 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) entries identified in Cell Ontology |
| quickOnto |
Probe the cache for entries found by bfcquery using the given query. |
| recognizedPredicates |
enumerate ontological relationships used in ontoProc utilities |
| search_labels |
use owlready2 ontology search facility on term labels |
| 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 |
| setup_entities |
construct owlents instance from an owl file |
| setup_entities2 |
preparing for a small number of entry points to owlready2 mediated by basilisk, this setup function will ingest OWL, enumerate classes and their names, and produce the 'parents' list, which can then be used with ontology_index to produce a functional ontology representation |
| 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 |
| subclasses |
retrieve subclass entities |
| 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 |
| 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 |
| [.owlents |
subset method |
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