calculate_rank_metric | Calculate rank metric for GSEA |
calculate_smart_text_size | Smart Text Size Calculator |
color_themes | Color Theme System for ggpicrust2 |
compare_daa_results | Compare the Consistency of Statistically Significant Features |
compare_gsea_daa | Compare GSEA and DAA results |
compare_metagenome_results | Compare Metagenome Results |
create_basic_go_mapping | Create basic GO mapping for microbiome analysis |
create_dendrogram | Create dendrogram plot from hierarchical clustering |
create_empty_plot | Create empty plot for edge cases |
create_gradient_colors | Create Gradient Colors |
create_heatmap_plot | Create heatmap visualization of GSEA results |
create_legend_theme | Create Enhanced Legend Theme |
create_network_plot | Create network visualization of GSEA results |
create_pathway_class_theme | Create Pathway Class Annotation Theme |
daa_annotated_results_df | Differentially Abundant Analysis Results with Annotation |
daa_results_df | DAA Results Dataset |
format_pvalue_smart | Smart P-value Formatting |
generate_nested_colors | Generate colors for nested grouping variables |
get_available_themes | Get Available Color Themes |
get_color_theme | Get Color Theme |
get_significance_colors | Get Significance Colors |
get_significance_stars | Get Significance Stars |
ggpicrust2 | This function integrates pathway name/description... |
ggpicrust2_extended | Integrated analysis with ggpicrust2 including GSEA |
gsea_pathway_annotation | Annotate GSEA results with pathway information |
import_MicrobiomeAnalyst_daa_results | Import Differential Abundance Analysis (DAA) results from... |
kegg_abundance | KEGG Abundance Dataset |
ko2kegg_abundance | Convert KO abundance in picrust2 export files to KEGG pathway... |
ko_abundance | KO Abundance Dataset |
legend_annotation_utils | Legend and Annotation Utilities for ggpicrust2 |
metacyc_abundance | MetaCyc Abundance Dataset |
metadata | Metadata for ggpicrust2 Demonstration |
pathway_annotation | Pathway information annotation |
pathway_daa | Differential Abundance Analysis for Predicted Functional... |
pathway_errorbar | The function pathway_errorbar() is used to visualize the... |
pathway_errorbar_table | Generate Abundance Statistics Table for Pathway Analysis |
pathway_gsea | Gene Set Enrichment Analysis for PICRUSt2 output |
pathway_heatmap | Create pathway heatmap with support for multiple grouping... |
pathway_pca | Perform Principal Component Analysis (PCA) on functional... |
prepare_gene_sets | Prepare gene sets for GSEA |
preview_color_theme | Preview Color Theme |
resolve_annotation_overlaps | Detect and Resolve Annotation Overlaps |
run_fgsea | Run fast GSEA implementation |
safe_extract | Safely Extract Elements from a List |
smart_color_selection | Smart Color Selection |
validate_abundance_data | Validate abundance data for PICRUSt compatibility |
validate_group_sizes | Validate group sizes for statistical analysis |
visualize_gsea | Visualize GSEA results |
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