Interactive Exploration of GSEA by the GOAT Method

---

Documentation for package ‘goatea’ version 0.99.9

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

Help Pages

calculate_geneSetRatio	Calculate geneSetRatio per gene per enrichment contrast
colorify	Create and/or modify color/gradient palettes
colorify_map	Colorify colorRamp between colors mapping to breakpoint values
display_palettes	Display R grDevices palettes
example_enrichment	An example enrichment
example_genelist	An example genelist
example_genesets	Example genesets
example_genes_overview	An example genes overview
example_ppi_data	An example ppi data
file_extension	Get file extension
filter_enrichment	Filter enrichment
get_base_folder	Set base folder
get_ppigraph	Get PPI igraph
get_string_ppi	Get STRING database Protein-Protein Interactions
get_terms_by_keywords	Get term names by searching with (partial) keywords
get_visNetwork	Get visNetwork graph
goatea_server	Server for goatea package
goatea_ui	UI for GOATEA package
hexcolor2rgba	Hex code colors to rgba format
palette_name_mapping	Palette original name mapping
plot_ComplexHeatmap	Plot ComplexHeatmap
plot_EnhancedVolcano	Plot EnhancedVolcano
plot_genelists_overlap_upsetjs	Visualize genelists gene overlap in an interactive UpSet plot
plot_gene_effectsize_ComplexHeatmap	Plot gene2effectsize ComplexHeatmap
plot_splitdot	Plot splitdot plot
plot_termtree	Plot semantic similarity termtree
process_string_input	Process Shiny area input string
read_validate_genelist	Read and validate a table with genes (that should be tested in overrepresentation-analysis) for compatibility with this R package#'
rename_gene_overview	Rename the gene overview
run_genelists_overlap	Create gene overview through overlapping genelists information by overlapping significant genes
run_geneset_enrichment	Perform geneset enrichment testing using any supported method
scale_values_between	Scale values between given min/max
set_significant_N_genes	Set significant and number of genes
wrap_hovertip	Wrap Shiny UI element with a hoverable tooltip contained in html div tags
wrap_loader	Wrap Shiny UI element with a loading spinner contained in html div tags