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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/ontoProc.html below:

Bioconductor - ontoProc (development version)

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 (3.22)

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] ORCID: 0000-0003-4046-0063 , Sara Stankiewicz [ctb], Victor Tarca [ctb] ORCID: 0009-0003-1976-0392

Maintainer: Vincent Carey <stvjc at channing.harvard.edu>

Citation (from within R, enter citation("ontoProc")): Installation

To install this package, start R (version "4.5") 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

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 Details biocViews GO, Infrastructure, Software Version 2.3.6 In Bioconductor since BioC 3.6 (R-3.4) (7.5 years) License Artistic-2.0 Depends R (>= 4.1), ontologyIndex Imports Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr, basilisk, jsonlite, RBGL, ellmer System Requirements 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 scDiffCom Links To Me Build Report Build Report Package Archives

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

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