ontoProc2
Ontology Facilities Based on INCAtools Semantic SQL
Bioconductor version: 3.24 · Package version: 0.99.32
This package provides ontology facilities based on INCAtools Semantic SQL. Tooling is provided to retrieve and cache SQLite databases representing curated ontologies. ontologyIndex ontology_index instances can be produced. Anthropic's Claude was used in the development of S7 classes and methods and in the production of documentation.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ontoProc2")Details
| Maintainer | Vincent Carey <stvjc@channing.harvard.edu> |
| Author | Vincent Carey [aut, cre] (ORCID: <https://orcid.org/0000-0003-4046-0063>), Anthropic-Claude Sonnet4.6 [eng], NIH NHGRI 2U24HG004059-17 [fnd] |
| License | Artistic-2.0 |
| URL | https://github.com/vjcitn/ontoProc2 |
| Bug Reports | https://github.com/vjcitn/ontoProc2/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataRepresentation, Infrastructure, Pathways, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/ontoProc2/ |
Citation
From within R, enter citation("ontoProc2"):
Vincent Carey. ontoProc2: Ontology Facilities Based on INCAtools Semantic SQL. doi:10.18129/B9.bioc.ontoProc2, R package version 0.99.32, https://bioconductor.org/packages/ontoProc2.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- celltoprotein -- connecting Cell and Protein Ontologies
- ontoProc2 -- leveraging semantic SQL for ontology analysis in Bioconductor
- uberonpeek -- a look at UBERON ontology, etc., with ontoProc2
Download
Follow the installation instructions to use this package in your R session.
| Source package | ontoProc2_0.99.32.tar.gz |
| Windows binary (x86_64) | ontoProc2_0.99.32.zip |
| macOS binary (arm64) | ontoProc2_0.99.32.tgz |
| macOS binary (x86_64) | ontoProc2_0.99.32.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: RSQLite, DBI, BiocFileCache, R.utils, dplyr, ontologyIndex, ontologyPlot, graph, Rgraphviz, igraph, ggraph, ggplot2, graphlayouts, grid, methods, S7, utils, httr2, xml2, digest
Suggests: knitr, testthat, BiocStyle, DT, GO.db, AnnotationDbi, stringr