Package: categoryCompare2 0.100.26
Robert M Flight
categoryCompare2: Meta-Analysis of High-Throughput Experiments Using Feature Annotations
Facilitates comparison of significant annotations (categories) generated on one or more feature lists. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
Authors:
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categoryCompare2.pdf |categoryCompare2.html✨
categoryCompare2/json (API)
NEWS
| # Install 'categoryCompare2' in R: |
| install.packages('categoryCompare2', repos = c('https://moseleybioinformaticslab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/moseleybioinformaticslab/categorycompare2/issues
annotationgomultiplecomparisonpathwaysgeneexpressionbioconductorbioinformaticsgene-annotationgene-expressiongene-sets
Last updated 19 days agofrom:9e757df39f (on v0.100.26). Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 30 2024 |
| R-4.5-win | WARNING | Oct 30 2024 |
| R-4.5-linux | WARNING | Oct 30 2024 |
| R-4.4-win | WARNING | Oct 30 2024 |
| R-4.4-mac | WARNING | Oct 30 2024 |
| R-4.3-win | WARNING | Oct 30 2024 |
| R-4.3-mac | WARNING | Oct 30 2024 |
Exports:annotationannotation_2_jsonannotation_combinationsannotation_gene_tableassign_colorsassign_communitiesbinomial_basicbinomial_feature_enrichmentbinomial_resultcc_graphcombine_annotation_featurescombine_annotationscombine_enrichmentscombine_textcombined_coefficientcombined_enrichmentcombined_significant_callscombined_statisticscsv_annotation_tableenriched_resultenriched_to_fgseaexecutable_pathextract_enrich_statsextract_statisticsfilter_annotation_graphgenerate_annotation_graphgenerate_annotation_similarity_graphgenerate_colorsgenerate_legendgenerate_linkgenerate_piechartsgenerate_tableget_db_annotationget_significant_annotationsget_significant_annotations_callsgocats_to_annotationgraph_to_visnetworkgsea_feature_enrichmenthypergeometric_basichypergeometric_feature_enrichmentinstall_executablesjaccard_coefficientjson_2_annotationjson_annotation_reversalkable_annotation_tablelabel_communitiesmulti_query_listnode_assignoverlap_coefficientremove_edgesshowsignificant_annotationsstatistical_resultstable_from_graphvis_in_cytoscapevis_visnetwork
Dependencies:AnnotationDbiaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIdplyrfansifastmapgenericsGenomeInfoDbGenomeInfoDbDataglueGO.dbgraphhttrigraphIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6rlangRSQLiteS4VectorssystibbletidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| add table data to graph | add_data_to_graph |
| add tooltip | add_tooltip |
| annotation class | annotation show,annotation-method |
| annotation to json | annotation_2_json |
| unique annotation combinations | annotation_combinations annotation_combinations,cc_graph-method annotation_combinations,significant_annotations-method |
| annotation to genes | annotation_gene_table |
| assign colors | assign_colors |
| assign communities | assign_communities |
| do binomial test | binomial_basic |
| do binomial testing | binomial_feature_enrichment |
| binomial feature class | binomial_features-class |
| the binomial results class | binomial_result binomial_result-class |
| categoryCompare2: A package for comparing enrichment results from multiple experiments | categoryCompare2 |
| cc_graph | cc_graph show,cc_graph-method |
| combine annotation-features | combine_annotation_features |
| combine annotations | combine_annotations combine_annotations,list-method |
| combine enrichments | combine_enrichments combine_enrichments,enriched_result-method combine_enrichments,list-method |
| combine text | combine_text |
| combined coefficient | combined_coefficient |
| combined enrichments | combined_enrichment combined_enrichment-class |
| get significant annotations calls | combined_significant_calls |
| combined statistics | combined_statistics |
| print table csv | csv_annotation_table |
| the enriched results class | enriched_result |
| convert enriched object | enriched_to_fgsea |
| executable path | executable_path |
| extract enrich stats | extract_enrich_stats |
| get statistics | extract_statistics extract_statistics,statistical_results-method |
| extract statistics | extract_statistics,combined_enrichment-method |
| filter graph by significant entries | filter_annotation_graph |
| generate annotation graph | generate_annotation_graph generate_annotation_graph,combined_enrichment-method |
| annotation similarity graph | generate_annotation_similarity_graph |
| generate colors | generate_colors |
| generate a legend | generate_legend |
| generate link text | generate_link |
| create piecharts for visualization | generate_piecharts |
| generate statistical table | generate_table generate_table,combined_enrichment-method |
| orgdb annotations | get_db_annotation |
| get significant annotations | get_significant_annotations get_significant_annotations,combined_enrichment-method get_significant_annotations,statistical_results-method |
| get significant annotations calls | get_significant_annotations_calls |
| gocats to annnotations | gocats_to_annotation |
| cc_graph to visnetwork | graph_to_visnetwork |
| do GSEA | gsea_feature_enrichment |
| GSEA feature class | gsea_features-class |
| hypergeom feature class | hypergeom_features-class |
| do hypergeometric test | hypergeometric_basic |
| do hypergeometric enrichment | hypergeometric_feature_enrichment |
| install executables | install_executables |
| jaccard coefficient | jaccard_coefficient |
| json to annotation | json_2_annotation |
| annotation reversal | json_annotation_reversal |
| print table kable | kable_annotation_table |
| label communities | label_communities |
| index a list | multi_query_list |
| node_assign | node_assign node_assign-class |
| overlap coefficient | overlap_coefficient |
| remove edges | remove_edges remove_edges,cc_graph,numeric-method remove_edges,character,numeric-method |
| show binomial_result | show,binomial_result-method |
| show combined_statistics | show,combined_statistics-method |
| show enriched_result | show,enriched_result-method |
| show node_assign | show,node_assign-method |
| show signficant_annotations | show,significant_annotations-method |
| significant annotations | significant_annotations |
| statistical results class | statistical_results statistical_results-class |
| table from graph | table_from_graph |
| visualize in cytoscape | vis_in_cytoscape |
| vis in visNetwork | vis_visnetwork |
