All functions

GeneTonic-pkg

GeneTonic

GeneTonic()

GeneTonic

GeneTonic_list()

Create a list for GeneTonic

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

describe_gtl()

Describe a GeneTonic list

deseqresult2df()

Generate a table from the DESeq2 results

distill_enrichment()

Distill enrichment results

.check_pandoc()

Check whether pandoc and pandoc-citeproc are available

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() gs_sankey()

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() gs_spider()

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_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