ontoProc2
This is the development version of ontoProc2; to use it, please install the devel version of Bioconductor.
Ontology Facilities Based on INCAtools Semantic SQL
Bioconductor version: Development (3.24)
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.
Author: Vincent Carey [aut, cre] 
, Anthropic-Claude Sonnet4.6 [eng], NIH NHGRI 2U24HG004059-17 [fnd]
Maintainer: Vincent Carey <stvjc at channing.harvard.edu>
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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ontoProc2")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ontoProc2")| celltoprotein -- connecting Cell and Protein Ontologies | HTML | R Script |
| ontoProc2 -- leveraging INCAtools semantic SQL for ontology analysis in Bioconductor | HTML | R Script |
| uberonpeek -- a look at UBERON ontology, etc., with ontoProc2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, Infrastructure, Pathways, SingleCell, Software |
| Version | 0.99.32 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| 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 |
| System Requirements | |
| URL | https://github.com/vjcitn/ontoProc2 |
| Bug Reports | https://github.com/vjcitn/ontoProc2/issues |
See More
| Suggests | knitr, testthat, BiocStyle, DT, GO.db, AnnotationDbi, stringr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (big-sur-x86_64) | ontoProc2_0.99.32.tgz |
| macOS Binary (sonoma-arm64) | ontoProc2_0.99.32.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ontoProc2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ontoProc2 |
| Package Short Url | https://bioconductor.org/packages/ontoProc2/ |
| Package Downloads Report | Download Stats |