Package: categoryCompare2 0.200.9

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:Robert M Flight [aut, cre], Hunter NB Moseley [aut], Erik D Huckvale [aut], Eugene W Hinderer [aut]

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manual.pdf |manual.html✨
card.svg |card.png
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

Pkgdown/docs site:https://moseleybioinformaticslab.github.io

On CRAN:

Conda:

annotationgomultiplecomparisonpathwaysgeneexpressionbioconductorbioinformaticsgene-annotationgene-expressiongene-sets

4.41 score 1 stars 10 scripts 58 exports 50 dependencies

Last updated from:6b39c9214a (on v0.200.9). Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK553
source / vignettesOK652
linux-release-x86_64OK516
macos-release-arm64OK586
macos-oldrel-arm64OK640
windows-develOK511
windows-releaseOK532
windows-oldrelOK497
wasm-releaseOK222

Exports:annotationannotation_2_jsonannotation_combinationsannotation_gene_tableassign_colorsassign_communitiesbinomial_basicbinomial_feature_enrichmentbinomial_featurescc_graphcombine_annotation_featurescombine_annotationscombine_enrichmentscombine_textcombined_coefficientcombined_enrichmentcombined_significant_callscombined_statisticscsv_annotation_tableexecutable_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_enrichmentgsea_featuresgsea_result_to_fgseahypergeometric_basichypergeometric_feature_enrichmenthypergeometric_featureshypergeometric_resultinstall_executablesjaccard_coefficientjson_2_annotationjson_annotation_reversalkable_annotation_tablelabel_communitiesmulti_query_listnode_assignoverlap_coefficientremove_edgesshowsignificant_annotationsstatistical_resultstable_from_graphvis_in_cytoscapevis_visnetwork

Dependencies:AnnotationDbiaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIdplyrfastmapgenericsglueGO.dbgraphhttrigraphIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigpngpurrrR6rlangRSQLiteS4VectorsSeqinfosystibbletidyselectutf8vctrswithrXVector

categoryCompare: High-throughput data meta-analysis using gene annotations, V2

Robert M Flight

Rendered fromv2_guide.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2026-05-04
Started: 2024-05-02

categoryCompare2: Command Line Interface

Rendered fromcommand_line_interface.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2025-06-30
Started: 2023-06-07

categoryCompare2: visNetwork

Rendered fromv2_visnetwork_guide.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2026-05-04
Started: 2024-05-02

Gene Set Enrichment Analysis

Robert M Flight

Rendered fromgsea.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2026-05-04
Started: 2024-10-31

Readme and manuals

Help Manual

Help pageTopics
add table data to graphadd_data_to_graph
add tooltipadd_tooltip
annotation classannotation show,annotation-method
annotation to jsonannotation_2_json
unique annotation combinationsannotation_combinations annotation_combinations,cc_graph-method annotation_combinations,significant_annotations-method
annotation to genesannotation_gene_table
assign colorsassign_colors
assign communitiesassign_communities
do binomial testbinomial_basic
do binomial testingbinomial_feature_enrichment
binomial_features constructorbinomial_features
binomial feature classbinomial_features-class
categoryCompare2: A package for comparing enrichment results from multiple experimentscategoryCompare2
cc_graphcc_graph show,cc_graph-method
combine annotation-featurescombine_annotation_features
combine annotationscombine_annotations combine_annotations,list-method
combine enrichmentscombine_enrichments combine_enrichments,enriched_result-method combine_enrichments,list-method
combine textcombine_text
combined coefficientcombined_coefficient
combined enrichmentscombined_enrichment combined_enrichment-class
get significant annotations callscombined_significant_calls
combined statisticscombined_statistics
print table csvcsv_annotation_table
the enriched results classbinomial_result binomial_result-class enriched_result enriched_result-class gsea_result gsea_result-class hypergeometric_result hypergeometric_result-class show,binomial_result-method show,enriched_result-method
executable pathexecutable_path
extract enrich statsextract_enrich_stats
get statisticsextract_statistics extract_statistics,statistical_results-method
extract statisticsextract_statistics,combined_enrichment-method
extract statisticsextract_statistics,enriched_result-method
filter graph by significant entriesfilter_annotation_graph
generate annotation graphgenerate_annotation_graph generate_annotation_graph,combined_enrichment-method
annotation similarity graphgenerate_annotation_similarity_graph
generate colorsgenerate_colors
generate a legendgenerate_legend
generate link textgenerate_link
create piecharts for visualizationgenerate_piecharts
generate statistical tablegenerate_table generate_table,combined_enrichment-method
orgdb annotationsget_db_annotation
get significant annotationsget_significant_annotations get_significant_annotations,combined_enrichment-method get_significant_annotations,statistical_results-method
get significant annotations callsget_significant_annotations_calls
gocats to annnotationsgocats_to_annotation
cc_graph to visnetworkgraph_to_visnetwork
do GSEAgsea_feature_enrichment
gsea_features constructorgsea_features
GSEA feature classgsea_features-class
convert gsea objectgsea_result_to_fgsea
do hypergeometric testhypergeometric_basic
do hypergeometric enrichmenthypergeometric_feature_enrichment
hypergeometric_features constructorhypergeometric_features
hypergeometric feature classhypergeometric_features-class
install executablesinstall_executables
jaccard coefficientjaccard_coefficient
json to annotationjson_2_annotation
annotation reversaljson_annotation_reversal
print table kablekable_annotation_table
label communitieslabel_communities
index a listmulti_query_list
node_assignnode_assign node_assign-class
overlap coefficientoverlap_coefficient
remove edgesremove_edges remove_edges,cc_graph,numeric-method remove_edges,character,numeric-method
show combined_statisticsshow,combined_statistics-method
show node_assignshow,node_assign-method
show signficant_annotationsshow,significant_annotations-method
significant annotationssignificant_annotations
statistical results classstatistical_results statistical_results-class
table from graphtable_from_graph
visualize in cytoscapevis_in_cytoscape
vis in visNetworkvis_visnetwork