Package index • goatea

All functions

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