Package index • categoryCompare2

All functions

add_data_to_graph(): add table data to graph

add_tooltip(): add tooltip

annotation() show(<annotation>): annotation class

annotation_2_json(): annotation to json

annotation_combinations(): unique annotation combinations

annotation_gene_table(): annotation to genes

assign_colors(): assign colors

assign_communities(): assign communities

binomial_basic(): do binomial test

binomial_feature_enrichment(): do binomial testing

binomial_features-class: binomial feature class

binomial_features(): binomial_features constructor

categoryCompare2: categoryCompare2: A package for comparing enrichment results from multiple experiments

cc_graph() show(<cc_graph>): cc_graph

combine_annotation_features(): combine annotation-features

combine_annotations(): combine annotations

combine_enrichments(): combine enrichments

combine_text(): combine text

combined_coefficient(): combined coefficient

combined_enrichment-class combined_enrichment: combined enrichments

combined_significant_calls(): get significant annotations calls

combined_statistics(): combined statistics

csv_annotation_table(): print table csv

hypergeometric_result() show(<enriched_result>) show(<binomial_result>): the enriched results class

executable_path(): executable path

extract_enrich_stats(): extract enrich stats

extract_statistics(<combined_enrichment>): extract statistics

extract_statistics(): get statistics

filter_annotation_graph(): filter graph by significant entries

generate_annotation_graph(): generate annotation graph

generate_annotation_similarity_graph(): annotation similarity graph

generate_colors(): generate colors

generate_legend(): generate a legend

generate_link(): generate link text

generate_piecharts(): create piecharts for visualization

generate_table(): generate statistical table

get_db_annotation(): orgdb annotations

get_significant_annotations(): get significant annotations

get_significant_annotations_calls(): get significant annotations calls

gocats_to_annotation(): gocats to annnotations

graph_to_visnetwork(): cc_graph to visnetwork

gsea_feature_enrichment(): do GSEA

gsea_features-class: GSEA feature class

gsea_features(): gsea_features constructor

gsea_result_to_fgsea(): convert gsea object

hypergeometric_basic(): do hypergeometric test

hypergeometric_feature_enrichment(): do hypergeometric enrichment

hypergeometric_features-class: hypergeometric feature class

hypergeometric_features(): hypergeometric_features constructor

install_executables(): install executables

jaccard_coefficient(): jaccard coefficient

json_2_annotation(): json to annotation

json_annotation_reversal(): annotation reversal

kable_annotation_table(): print table kable

label_communities(): label communities

multi_query_list(): index a list

node_assign-class node_assign: node_assign

overlap_coefficient(): overlap coefficient

remove_edges(): remove edges

show(<combined_statistics>): show combined_statistics

show(<node_assign>): show node_assign

show(<significant_annotations>): show signficant_annotations

significant_annotations(): significant annotations

statistical_results-class statistical_results: statistical results class

table_from_graph(): table from graph

vis_in_cytoscape(): visualize in cytoscape

vis_visnetwork(): vis in visNetwork