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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | 0.99.30 |
| 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, 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ontoProc2_0.99.30.tar.gz |
| Windows Binary (x86_64) | ontoProc2_0.99.28.zip |
| macOS Binary (big-sur-x86_64) | ontoProc2_0.99.30.tgz |
| macOS Binary (sonoma-arm64) | ontoProc2_0.99.30.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ontoProc2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ontoProc2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ontoProc2/ |
| Package Short Url | https://bioconductor.org/packages/ontoProc2/ |
| Package Downloads Report | Download Stats |