Interactive Exploration of GSEA by the GOAT Method


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Documentation for package ‘goatea’ version 0.99.9

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