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ontoProc

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

Bioconductor version: 3.23 · Package version: 2.6.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ontoProc")

Details

MaintainerVincent Carey <stvjc@channing.harvard.edu>
AuthorVincent Carey [ctb, cre] (ORCID: <https://orcid.org/0000-0003-4046-0063>), Sara Stankiewicz [ctb], Victor Tarca [ctb] (ORCID: <https://orcid.org/0009-0003-1976-0392>)
LicenseArtistic-2.0
URLhttps://github.com/vjcitn/ontoProc
Bug Reportshttps://github.com/vjcitn/ontoProc/issues
Downloads rank462
Source branchRELEASE_3_23
biocViewsGO, Infrastructure, Software

Documentation

Download

Dependencies

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

Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick

Reverse dependencies

Imports Me (2): pogos, tenXplore

Suggests Me (2): scConform, scDiffCom