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 (from within R, enter 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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

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

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 git@git.bioconductor.org: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