ontoProc

DOI: 10.18129/B9.bioc.ontoProc    

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

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

HTML R Script ontoProc: some ontology-oriented utilites with single-cell focus for Bioconductor
PDF   Reference Manual
Text   NEWS

Details

biocViews GO, Infrastructure, Software
Version 1.20.0
In Bioconductor since BioC 3.6 (R-3.4) (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
LinkingTo
Suggests knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi
SystemRequirements
Enhances
URL https://github.com/vjcitn/ontoProc
BugReports https://github.com/vjcitn/ontoProc/issues
Depends On Me SingleRBook
Imports Me pogos, tenXplore
Suggests Me BiocOncoTK
Links To Me
Build Report  

Package Archives

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

Source Package ontoProc_1.20.0.tar.gz
Windows Binary ontoProc_1.20.0.zip (64-bit only)
macOS Binary (x86_64) ontoProc_1.20.0.tgz
macOS Binary (arm64) ontoProc_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ontoProc
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ontoProc
Package Short Url https://bioconductor.org/packages/ontoProc/
Package Downloads Report Download Stats

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