Man pages for paulklemm/mygo
Create Report for mus musculus dataset of GO-term analysis using clusterProfiler

add_is_duplicatedCheck if rowname is duplicated and add binary is_duplicated...
attach_goterm_genecountAdd count for each GO-term and calculate overlap ratio of...
bind_goterm_tableCombine goterms into a single data frame
createHTMLReportMake GO-Term analysis and print out Report
emap_plotCreate clusterProfiler EMA plot from go term
emap_plot_facet_categoryCombine emap plots into one ggplot2 plot
export_go_terms_to_excelExport list of GO terms to Excel file
get_go_all_ontologiesGet GO-terms for all ontologies
get_go_all_ontologies_2Get GO-terms for all ontologies. This method requires a...
get_go_all_ontologies_helperHelper function getting all GO-terms based on vectors of...
get_gse_all_ontologiesGet GSE-terms for all ontologies
get_keggGet KEGG GSE terms
get_kegg_tableGet Table containing Kegg pathway information 'pathway',...
get_named_fc_vectorGet named fc vector. Prepare input data as required by GSE
overlap_percentage_plotPlot top n GO-terms w.r.t percentage of significant genes...
overlap_percentage_plot_facet_categoryWrapper for mygo::overlap_percentage_plot to facet all GO...
overlap_scatterplotPlot total gene count against percentage of significant genes
perform_enrichGOPerform a clusterPrfiler enrichGO analysis
perform_gseGOPerform a clusterProfiler gseGO analysis
perform_gseKEGGPerform a clusterProfiler gseKEGG analysis
plot_all_ontologiesPrint a couple of standard plots for provided GO ontologies
plot_keggCreate KEGG pathway as PNG
plot_pngPlot png object (e.g. from plot_kegg_pathway)
plot_terms_goPrint a series of clusterProfiler plots
plot_terms_gsePlot GSE terms
print_goterm_as_datatableHelper function, takes clusterProfiler GO-term result and...
run_gotermsRun GO-Term analysis and retrieve plots This is for usage in...
simplify_ontologiesSimplify GO terms
volcano_plotReturn a volcano plot with annotated top_n values
paulklemm/mygo documentation built on July 27, 2023, 11:36 a.m.