# Interactive Exploration of GSEA by the GOAT Method

## Documentation for package ‘goatea’ version 1.0.0

- 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