# Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

## Documentation for package ‘GeneTonic’ version 3.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.check_pandoc | Check whether 'pandoc' and 'pandoc-citeproc' are available
checkup_GeneTonic | Checking the input objects for GeneTonic
checkup_gtl | Checking the 'gtl' input object for GeneTonic
check_colors | Check colors
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
geneinfo_2_html | Information on a gene
GeneTonic | GeneTonic
GeneTonicList | Create a GeneTonicList object
GeneTonic_list | Create a GeneTonicList object
gene_plot | Plot expression values for 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
gostres_macrophage | A sample output from g:Profiler
go_2_html | Information on a GeneOntology identifier
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_sankey | Alluvial (sankey) plot for a set of genesets and the associated genes
gs_scores | Compute gene set scores
gs_scoresheat | Plots a matrix of geneset scores
gs_simplify | Simplify results from functional enrichment analysis
gs_spider | Radar (spider) plot for gene sets
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