Package: ontoFAST 1.0.1

ontoFAST: Interactive Annotation of Characters with Biological Ontologies

Tools for annotating characters (character matrices) with anatomical and phenotype ontologies. Includes functions for visualising character annotations and creating simple queries using ontological relationships.

Authors:Sergei Tarasov

ontoFAST_1.0.1.tar.gz
ontoFAST_1.0.1.zip(r-4.5)ontoFAST_1.0.1.zip(r-4.4)ontoFAST_1.0.1.zip(r-4.3)
ontoFAST_1.0.1.tgz(r-4.4-any)ontoFAST_1.0.1.tgz(r-4.3-any)
ontoFAST_1.0.1.tar.gz(r-4.5-noble)ontoFAST_1.0.1.tar.gz(r-4.4-noble)
ontoFAST_1.0.1.tgz(r-4.4-emscripten)ontoFAST_1.0.1.tgz(r-4.3-emscripten)
ontoFAST.pdf |ontoFAST.html✨
ontoFAST/json (API)

# Install 'ontoFAST' in R:

install.packages('ontoFAST', repos = c('https://sergeitarasov.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sergeitarasov/ontofast/issues

Datasets:

HAO - Hymenoptera Anatomy Ontology
Scarab - A modified Hymenoptera Anatomy Ontology (HAO) to accommodate anatomy of dung beetles
Sharkey_2011 - Hymenoptera character statements
Sharkey_2011_annot - Hymenoptera characters annotated with ontology terms
Tarasov_2017_annot - Dung beetle characters annotated with ontology terms
exclude_terms - Ontology terms to exclude for sunburst plot

On CRAN:

annotations character-matrices characters ontology phylogenetics

3.00 score 2 stars 5 scripts 113 downloads 17 exports 76 dependencies

Last updated 2 years agofrom:c4e12584fd. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 22 2024
R-4.5-win	OK	Oct 22 2024
R-4.5-linux	OK	Oct 22 2024
R-4.4-win	NOTE	Oct 22 2024
R-4.4-mac	NOTE	Oct 22 2024
R-4.3-win	NOTE	Oct 22 2024
R-4.3-mac	NOTE	Oct 22 2024

Exports:annot_all_chars annot_char_grep chars_per_term edges2list export_annotations export_cytoscape get_ancestors_chars get_descendants_chars get_onto_id get_onto_name list2edges make_shiny_in onto_process paths_sunburst runOntoFast syn_extract table2list

Dependencies:askpass base64enc bslib cachem cli clipr commonmark cpp11 crayon credentials curl d3r desc digest dplyr evaluate fansi fastmap fontawesome fs generics gert gh gitcreds glue highr htmltools htmlwidgets httpuv httr2 ini jquerylib jsonlite knitr later lifecycle magrittr memoise mime ontologyIndex openssl pbapply pillar pkgconfig plyr promises purrr R6 rappdirs Rcpp rlang rmarkdown rprojroot rstudioapi sass shiny shinydashboard sourcetools stringi stringr sunburstR sys tibble tidyr tidyselect tinytex usethis utf8 vctrs visNetwork whisker withr xfun xtable yaml zip

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate all character statements with ontology terms	annot_all_chars
Annotate a character statement with ontology terms	annot_char_grep
Get number of chracters per each ontology term	chars_per_term
Convert edge matrix to list	edges2list
Ontology terms to exclude for sunburst plot	exclude_terms
Export annotation data	export_annotations
Export to Cytoscape format	export_cytoscape
Get ancestal ontology terms for a set of characters	get_ancestors_chars
Get characters that descendants of selected ontology term	get_descendants_chars
Get IDs for ontology names	get_onto_id
Get names for ontology IDs	get_onto_name
Hymenoptera Anatomy Ontology (HAO)	HAO
Convert list to edge matrix	list2edges
Make an ontology object for visualization	make_shiny_in
Shortcut to process characters and ontology	onto_process
Return ontology paths for characters	paths_sunburst
Run ontoFAST interactively	runOntoFast
A modified Hymenoptera Anatomy Ontology (HAO) to accommodate anatomy of dung beetles	Scarab
Hymenoptera character statements	Sharkey_2011
Hymenoptera characters annotated with ontology terms	Sharkey_2011_annot
Link synonyms with ontology terms	syn_extract
Converts a table to list	table2list
Dung beetle characters annotated with ontology terms	Tarasov_2017_annot