All functions |
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produce a data.frame of features relevant to a Cell Ontology class |
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PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology |
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manage ontological data with tags and a DataFrame instance |
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allGOterms: data.frame with ids and terms |
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retrieve ancestor 'sets' |
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obtain list of names of a set of ancestors |
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add mapping from informal to formal cell type tags to a SummarizedExperiment colData |
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combine TermSet instances |
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utilities for approximate matching of cell type terms to GO categories and annotations |
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obtain list of names of a set of subclasses/children |
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obtain named character vector of terms from Cell Line Ontology, omitting obsolete and trailing 'cell' |
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list and count samples with common ontological annotation in two SEs |
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connect ontological categories between related, annotated SummarizedExperiments |
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app to review molecular properties of cell types via cell ontology |
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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 |
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demonstrate the use of makeSelectInput |
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dropStop is a utility for removing certain words from text data |
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some fields of interest are lists, and grep per se should not be used -- this function checks and uses grep within vapply when appropriate |
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Find common ancestors |
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basic getters in old style, retained 2023 for deprecation interval |
obtain childless descendents of a term (including query) |
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get the ontology based on a short tag and year |
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return a generator with ontology classes |
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decompress ordo owl file |
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humrna: a data.frame of SRA metadata related to RNA-seq in humans |
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inject linefeeds for node names for graph, with textual annotation from ontology |
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retrieve labels with names |
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use output of cyclicSigset to generate a series of character vectors constituting OBO terms |
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Produce a data.frame with a set of naive terms mapped to all matching ontology ids and their formal terms |
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generate a selectInput control for an ontologyIndex slice |
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obtain graphNEL from ontology_plot instance of ontologyPlot |
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use prose terminology with output of connect_classes |
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use grep or agrep to find a match for a naive token into ontology |
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minicorpus: a vector of annotation strings found in 'study title' of SRA metadata. |
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repair nomenclature mismatches (to curated term set) in a vector of terms |
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high-level use of graph/Rgraphviz for rendering ontology relations |
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list parentless nodes in ontology_index instance |
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cache an owl file accessible via URL |
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packDesc2019: overview of ontoProc resources |
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packDesc2021: overview of ontoProc resources |
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packDesc2022: overview of ontoProc resources |
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packDesc2023: overview of ontoProc resources |
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retrieve is_a |
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visualize ontology selection via onto_plot2, based on owlents |
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short printer |
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enumerate ontological relationships used in ontoProc utilities |
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simple generation of children of 'choices' given as terms, returned as TermSet |
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select a set of elements from a term 'map' and return a contribution to a data.frame |
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construct owlents instance from an owl file |
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tabulate the basic outcome of PBMC 3K tutorial of Seurat |
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generate a TermSet with siblings of a given term, excluding that term by default |
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stopWords: vector of stop words from xpo6.com |
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subset method |
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retrieve subclass entities |
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subset a SummarizedExperiment to which ontology tags have been bound using 'bind_formal_tags', obtaining the 'descendants' of the class of interest |
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use Cell Ontology and Protein Ontology to identify cell-type defining conditions in which a given gene is named |
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check that a URL can get a 200 for a HEAD request |
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give a vector of valid 'names' of ontoProc ontologies |