Package: simona 1.11.0

Zuguang Gu

simona: Semantic Similarity on Bio-Ontologies

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

Authors:Zuguang Gu [aut, cre]

simona_1.11.0.tar.gz
simona_1.11.0.zip(r-4.7)simona_1.11.0.zip(r-4.6)simona_1.11.0.zip(r-4.5)
simona_1.11.0.tgz(r-4.6-x86_64)simona_1.11.0.tgz(r-4.6-arm64)simona_1.11.0.tgz(r-4.5-x86_64)simona_1.11.0.tgz(r-4.5-arm64)
simona_1.11.0.tar.gz(r-4.7-arm64)simona_1.11.0.tar.gz(r-4.7-x86_64)simona_1.11.0.tar.gz(r-4.6-arm64)simona_1.11.0.tar.gz(r-4.6-x86_64)
simona_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
simona/json (API)

# Install 'simona' in R:

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

Bug tracker:https://github.com/jokergoo/simona/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:simona-1.11.0(bioc 3.24)simona-1.10.0(bioc 3.23)

software annotation go biomedicalinformatics cpp

7.15 score 18 stars 2 packages 44 scripts 94 exports 61 dependencies

Last updated from:7a56b7d497. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	315
linux-devel-arm64	NOTE	341
linux-devel-x86_64	NOTE	445
source / vignettes	OK	465
linux-release-arm64	NOTE	336
linux-release-x86_64	NOTE	410
macos-release-arm64	NOTE	235
macos-release-x86_64	NOTE	433
macos-oldrel-arm64	NOTE	226
macos-oldrel-x86_64	NOTE	599
windows-devel	NOTE	341
windows-release	NOTE	298
windows-oldrel	NOTE	337
wasm-release	OK	286

Exports:add_annotation all_group_sim_methods all_term_IC_methods all_term_sim_methods alternative_GO_terms annotated_terms avg_children avg_parents CA_terms create_ontology_DAG create_ontology_DAG_from_GO_db create_ontology_DAG_from_igraph dag_add_random_children dag_all_terms dag_ancestors dag_as_dendrogram dag_as_DOT dag_as_igraph dag_children dag_circular_viz dag_depth dag_distinct_ancestors dag_enrich_on_genes dag_enrich_on_items dag_enrich_on_offsprings dag_filter dag_graphviz dag_has_terms dag_height dag_is_leaf dag_leaves dag_longest_dist_from_ancestors dag_longest_dist_to_offspring dag_n_leaves dag_n_relations dag_n_terms dag_offspring dag_parents dag_permutate_children dag_random dag_random_tree dag_reorder dag_root dag_shiny dag_shortest_dist_from_ancestors dag_shortest_dist_from_root dag_shortest_dist_to_leaves dag_shortest_dist_to_offspring dag_siblings dag_treelize group_sim import_obo import_ontology import_owl import_ttl LCA_depth LCA_term longest_distances_directed longest_distances_via_LCA max_ancestor_id max_ancestor_path_sum max_ancestor_v mcols mcols<-method_param MICA_IC MICA_term n_ancestors n_annotations n_children n_connected_leaves n_offspring n_parents NCA_term ontology_chebi ontology_DAG ontology_go ontology_hp ontology_kw ontology_pw ontology_rdo ontology_reactome ontology_vt partition_by_level partition_by_size random_items random_terms shortest_distances_directed shortest_distances_via_NCA show simona_opt term_annotations term_IC term_sim

Dependencies:base64enc BiocGenerics bslib cachem circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap cpp11 crayon digest doParallel fastmap fastmatch fontawesome foreach fs generics GetoptLong GlobalOptions glue htmltools httpuv igraph IRanges iterators jquerylib jsonlite later lattice lifecycle magrittr Matrix matrixStats memoise mime otel pkgconfig png Polychrome promises R6 rappdirs RColorBrewer Rcpp rjson rlang S4Vectors sass scatterplot3d shape shiny sourcetools vctrs withr xml2 xtable

The simona package

Rendered fromsimona.Rmdusingknitr::rmarkdown

Last update: 2024-02-27
Started: 2024-02-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create sub-DAGs	[,ontology_DAG,ANY,ANY,ANY-method [,ontology_DAG,ANY,ANY,missing-method [,ontology_DAG,ANY,missing,ANY-method [,ontology_DAG,ANY,missing,missing-method [,ontology_DAG,missing,ANY,ANY-method [,ontology_DAG,missing,ANY,missing-method [,ontology_DAG,missing,missing,ANY-method [,ontology_DAG,missing,missing,missing-method [[,ontology_DAG,character,missing-method
Add annotations to the DAG object	add_annotation
Supported methods	all_group_sim_methods all_term_IC_methods all_term_sim_methods
Create the ontology_DAG object	create_ontology_DAG
Create the ontology_DAG object from the GO.db package	alternative_GO_terms create_ontology_DAG_from_GO_db
Create the ontology_DAG object from the igraph object	create_ontology_DAG_from_igraph
Names of all terms	dag_all_terms dag_n_leaves dag_n_relations dag_n_terms
Convert to an igraph object	dag_as_igraph
Visualize the DAG	dag_as_DOT dag_circular_viz dag_graphviz
Depth and height in the DAG	dag_depth dag_height dag_shortest_dist_from_root dag_shortest_dist_to_leaves
Distinct ancestors of a list of terms	dag_distinct_ancestors
Enrichment analysis on the number of annotated items	dag_enrich_on_genes dag_enrich_on_items
Enrichment analysis on offspring terms	dag_enrich_on_offsprings
Enrichment analysis on offspring terms by permutation test	dag_enrich_on_offsprings_by_permutation
Filter the DAG	dag_filter
Whether the terms exist in the DAG	dag_has_terms
Distance from all ancestors/to all offspring in the DAG	dag_longest_dist_from_ancestors dag_longest_dist_to_offspring dag_shortest_dist_from_ancestors dag_shortest_dist_to_offspring
Parent/child/ancestor/offspring terms	dag_ancestors dag_children dag_offspring dag_parents dag_siblings
Generate a random DAG	dag_add_random_children dag_random dag_random_tree
Reorder the DAG	dag_permutate_children dag_reorder
Root or leaves of the DAG	dag_is_leaf dag_leaves dag_root
A shiny app for the DAG	dag_shiny
Reduce the DAG to a tree	dag_as_dendrogram dag_treelize print.ontology_tree
Semantic similarity between two groups of terms	group_sim
Import ontology file to an ontology_DAG object	import_obo import_ontology import_owl import_ttl
Get or set meta columns on DAG	mcols,ontology_DAG-method mcols<-,ontology_DAG-method
All Papameters of a given method	method_param
Various types of common ancestors	CA_terms LCA_depth LCA_term max_ancestor_id max_ancestor_path_sum max_ancestor_v MICA_IC MICA_term NCA_term
Number of annotated items	has_annotation n_annotations
Number of parent/child/ancestor/offspring/leaf terms	avg_children avg_parents n_ancestors n_children n_connected_leaves n_offspring n_parents
The ontology_DAG class	ontology_DAG ontology_DAG-class
Import ontologies already having gene annotations	ontology_chebi ontology_go ontology_hp ontology_kw ontology_pw ontology_rdo ontology_reactome ontology_vt
Partition the DAG	partition_by_level partition_by_size
Print the source	print.print_source
Randomly sample terms/items	random_items random_terms
Distance on the DAG	longest_distances_directed longest_distances_via_LCA shortest_distances_directed shortest_distances_via_NCA
Print the ontology_DAG object	show,ontology_DAG-method
Global options	simona_opt
Term-item associations	annotated_terms term_annotations
Information content	term_IC
Semantic similarity	term_sim