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 |