Package: simona 1.5.0
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:
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simona.pdf |simona.html✨
simona/json (API)
NEWS
| # 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
On BioConductor:simona-1.5.0(bioc 3.21)simona-1.4.0(bioc 3.20)
softwareannotationgobiomedicalinformatics
Last updated 25 days agofrom:40a2e14c42. Checks:OK: 1 NOTE: 3 WARNING: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 31 2024 |
Exports:add_annotationall_group_sim_methodsall_term_IC_methodsall_term_sim_methodsalternative_GO_termsannotated_termsavg_childrenavg_parentsCA_termscreate_ontology_DAGcreate_ontology_DAG_from_GO_dbcreate_ontology_DAG_from_igraphdag_add_random_childrendag_all_termsdag_ancestorsdag_as_dendrogramdag_as_DOTdag_as_igraphdag_childrendag_circular_vizdag_depthdag_distinct_ancestorsdag_enrich_on_genesdag_enrich_on_itemsdag_enrich_on_offspringsdag_filterdag_graphvizdag_has_termsdag_heightdag_is_leafdag_leavesdag_longest_dist_from_ancestorsdag_longest_dist_to_offspringdag_n_leavesdag_n_relationsdag_n_termsdag_offspringdag_parentsdag_permutate_childrendag_randomdag_random_treedag_reorderdag_rootdag_shinydag_shortest_dist_from_ancestorsdag_shortest_dist_from_rootdag_shortest_dist_to_leavesdag_shortest_dist_to_offspringdag_siblingsdag_treelizegroup_simimport_oboimport_ontologyimport_owlimport_ttlLCA_depthLCA_termlongest_distances_directedlongest_distances_via_LCAmax_ancestor_idmax_ancestor_path_summax_ancestor_vmcolsmcols<-method_paramMICA_ICMICA_termn_ancestorsn_annotationsn_childrenn_connected_leavesn_offspringn_parentsNCA_termontology_chebiontology_DAGontology_goontology_hpontology_kwontology_pwontology_rdoontology_vtpartition_by_levelpartition_by_sizerandom_itemsrandom_termsshortest_distances_directedshortest_distances_via_NCAshowsimona_optterm_annotationsterm_ICterm_sim
Dependencies:base64encBiocGenericsbslibcachemcirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcpp11crayondigestdoParallelfastmapfontawesomeforeachfsGetoptLongGlobalOptionsgluehtmltoolshttpuvigraphIRangesiteratorsjquerylibjsonlitelaterlatticelifecyclemagrittrMatrixmatrixStatsmemoisemimepkgconfigpngPolychromepromisesR6rappdirsRColorBrewerRcpprjsonrlangS4Vectorssassscatterplot3dshapeshinysourcetoolsvctrswithrxml2xtable
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_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 |
