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
| Maintainer | Vincent Carey <stvjc@channing.harvard.edu> |
| Author | Vincent 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>) |
| License | Artistic-2.0 |
| URL | https://github.com/vjcitn/ontoProc |
| Bug Reports | https://github.com/vjcitn/ontoProc/issues |
| Downloads rank | 462 |
| Source branch | RELEASE_3_23 |
| biocViews | GO, Infrastructure, Software |
Documentation
- ontoProc: Ontology interfaces for Bioconductor, with focus on cell type identification
- owlents: using OWL directly in ontoProc
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