.check_pandoc           Check whether 'pandoc' and 'pandoc-citeproc'
                        are available
GeneTonic               GeneTonic
GeneTonicList           Create a GeneTonicList object
check_colors            Check colors
checkup_GeneTonic       Checking the input objects for GeneTonic
checkup_gtl             Checking the 'gtl' input object for GeneTonic
cluster_markov          Markov Clustering (MCL) for community detection
create_jaccard_matrix   Compute the overlap matrix for enrichment
                        results
create_kappa_matrix     Compute the kappa matrix for enrichment results
create_upsetdata        Create a geneset upset dataset
deprecated              Deprecated functions in GeneTonic
describe_gtl            Describe a GeneTonic list
deseqresult2df          Generate a table from the 'DESeq2' results
distill_enrichment      Distill enrichment results
editor_to_vector_sanitized
                        Extract vectors from editor content
enhance_table           Visually enhances a functional enrichment
                        result table
enrichment_map          Creates an enrichment map for the results of
                        functional enrichment
enrichr_output_macrophage
                        A sample output from Enrichr
export_for_iSEE         export_for_iSEE
export_to_sif           Export to sif
fgseaRes                A sample output from fgsea
gene_plot               Plot expression values for a gene
geneinfo_2_html         Information on a gene
get_aggrscores          Compute aggregated scores for gene sets
get_expression_values   Get expression values
ggs_backbone            Extract the backbone for the gene-geneset graph
ggs_graph               Construct a gene-geneset-graph
go_2_html               Information on a GeneOntology identifier
gostres_macrophage      A sample output from g:Profiler
gs_alluvial             Alluvial (sankey) plot for a set of genesets
                        and the associated genes
gs_dendro               Dendrogram of the gene set enrichment results
gs_fuzzyclustering      Compute fuzzy clusters of gene sets
gs_heatmap              Plot a heatmap of the gene signature on the
                        data
gs_horizon              Plots a summary of enrichment results
gs_mds                  Multi Dimensional Scaling plot for gene sets
gs_radar                Radar (spider) plot for gene sets
gs_scores               Compute gene set scores
gs_scoresheat           Plots a matrix of geneset scores
gs_simplify             Simplify results from functional enrichment
                        analysis
gs_summary_heat         Plots a heatmap for genes and genesets
gs_summary_overview     Plots a summary of enrichment results
gs_summary_overview_pair
                        Plots a summary of enrichment results
gs_upset                Upset plot for genesets
gs_volcano              Volcano plot for gene sets
happy_hour              Happy hour!
map2color               Maps numeric values to color values
overlap_coefficient     Calculate overlap coefficient
overlap_jaccard_index   Calculate Jaccard Index between two sets
res_macrophage_IFNg_vs_naive
                        A sample 'DESeqResults' object
shake_davidResult       Convert the output of DAVID
shake_enrichResult      Convert an enrichResult object
shake_enrichrResult     Convert the output of Enrichr
shake_fgseaResult       Convert the output of fgsea
shake_gprofilerResult   Convert the output of g:Profiler
shake_gsenrichResult    Convert a gseaResult object
shake_topGOtableResult
                        Convert a topGOtableResult object
signature_volcano       Plot a volcano plot of a geneset
styleColorBar_divergent
                        Style DT color bars
summarize_ggs_hubgenes
                        Summarize information on the hub genes
topgoDE_macrophage_IFNg_vs_naive
                        A sample 'res_enrich' object
