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ontoProc

This is the development version of ontoProc; for the stable release version, see ontoProc.

processing of ontologies of anatomy, cell lines, and so on


Bioconductor version: Development (3.20)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ontoProc")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GO, Infrastructure, Software
Version 1.27.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64) ontoProc_1.27.0.tgz
macOS Binary (arm64)
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