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| 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 |