allGOterms |
allGOterms: data.frame with ids and terms |
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' |
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 |
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 |
getEFOOnto |
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 |
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 |
label_TAG |
generate a TermSet with siblings of a given term, excluding that term by default |
makeSelectInput |
generate a selectInput control for an ontologyIndex slice |
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 |
secLevGen |
simple generation of children of 'choices' given as terms, returned as TermSet |
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 |
TermSet-class |
manage ontological data with tags and a DataFrame instance |