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CLfeats()
produce a data.frame of features relevant to a Cell Ontology class
PROSYM
PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
show(<TermSet> )
manage ontological data with tags and a DataFrame instance
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
bioregistry_ols_resources()
produce bioregistry_ols table
c(<TermSet> )
combine TermSet instances
cellTypeToGO() cellTypeToGenes()
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
cleanCLOnames()
obtain named character vector of terms from Cell Line Ontology, omitting obsolete and trailing 'cell'
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
getChebiLite() getCellosaurusOnto() getUBERON_NE() getChebiOnto() getOncotreeOnto() getDiseaseOnto() getGeneOnto() getHCAOnto() getPROnto() getPATOnto() getMondoOnto() getSIOOnto()
basic getters in old style, retained 2023 for deprecation interval
getLeavesFromTerm()
obtain childless descendents of a term (including query)
getOnto()
get the ontology based on a short tag and year
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
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
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
siblings_TAG() label_TAG() children_TAG()
generate a TermSet with siblings of a given term, excluding that term by default
stopWords
stopWords: vector of stop words from xpo6.com
`[`(<owlents> )
subset method
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
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