| 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 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_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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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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