ontoProc
processing of ontologies of anatomy, cell lines, and so on
Bioconductor version: Release (3.19)
Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.
Author: Vincent Carey [ctb, cre] 
, Sara Stankiewicz [ctb]
Maintainer: Vincent Carey <stvjc at channing.harvard.edu>
citation("ontoProc")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ontoProc")
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("ontoProc")| ontoProc: some ontology-oriented utilites with single-cell focus for Bioconductor | HTML | R Script |
| owlents: using OWL directly in ontoProc | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GO, Infrastructure, Software |
| Version | 1.26.4 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), ontologyIndex |
| Imports | Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr |
| System Requirements | owlready2 |
| URL | https://github.com/vjcitn/ontoProc |
| Bug Reports | https://github.com/vjcitn/ontoProc/issues |
See More
| Suggests | knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick |
| Linking To | |
| Enhances | |
| Depends On Me | SingleRBook |
| Imports Me | pogos, tenXplore |
| Suggests Me | BiocOncoTK, scDiffCom |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ontoProc_1.26.4.tar.gz |
| Windows Binary (x86_64) | ontoProc_1.26.4.zip |
| macOS Binary (x86_64) | ontoProc_1.26.4.tgz |
| macOS Binary (arm64) | ontoProc_1.26.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ontoProc |
| Source Repository (Developer Access) | git clone [email protected]:packages/ontoProc |
| Bioc Package Browser | https://code.bioconductor.org/browse/ontoProc/ |
| Package Short Url | https://bioconductor.org/packages/ontoProc/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |