Combat_Normal           Process and Correct Batch Effects in TCGA's
                        normal tissue and GTEX Data
Contrast_Venn           Function to Create a Venn Diagram of DEGs with
                        Custom Colors
DESeq2_analyze          Differential Gene Expression Analysis using
                        'DESeq2'
Wilcoxon_analyze        Differential Gene Expression Analysis Using
                        Wilcoxon Rank-Sum Test
add_boxplot             Add a boxplot layer to a 'ggtree' plot
adjust_alpha_scale      Adjust Alpha Scale for Data Visualization
adjust_color_tone       Adjust Color Tone by Modifying Saturation and
                        Luminance
adjust_export_pathway   Adjust and Export Pathway Analysis Results
all_degs_venn           All DEGs Venn Diagram Data
combat_tumor            Process and Correct Batch Effects in Tumor Data
compare_merge           Compare and merge specific columns from two DEG
                        data frames
create_base_plot        Create a base plot with gene expression data on
                        a phylogenetic tree
deg_filter              Function to Filter Differentially Expressed
                        Genes (DEGs)
drawLegends             Draw Dual-Sided Legends on a Plot
edgeR_analyze           Differential Gene Expression Analysis using
                        'edgeR'
enrich_circo_bar        Combine and Visualize Data with Circular Bar
                        Chart
enrich_polar_bubble     Enrichment Polar Bubble Plot
enrichment_circlize     Draw Chord Diagram with Legends
enrichment_spiral_plots
                        Create Spiral Plots with Legends Using
                        'spiralize' and 'ComplexHeatmap'
extract_descriptions_counts
                        Extract and Count Descriptions with Specified
                        Color
extract_ntop_pathways   Extract and Store Top Pathways for Each Sample
extract_positive_pathways
                        Extract Positive Pathways from SSGSEA Results
                        and Select Random Samples
facet_density_foldchange
                        Create faceted high-density region plots with
                        optional points and density contours
filter_diff_genes       Filter Differentially Expressed Genes
four_degs_venn          Function to Create a Venn Diagram of DEGs
gather_graph_edge       Gather graph edge from data frame Please note
                        that this function is from the 'ggraph' package
                        and has not been altered in functionality, but
                        it has been optimized and iterated. It is not
                        original content of 'TransProR'. However, since
                        'ggraph' caused frequent GitHub Action errors
                        during the creation of 'TransProR', the author
                        directly referenced the involved functions in
                        'TransProR'. This is not the author's original
                        creation. All users please be aware!
gather_graph_node       Gather graph nodes from a data frame Please
                        note that this function is from the 'ggraph'
                        package and has not been altered in
                        functionality, but it has been optimized and
                        iterated. It is not original content of
                        'TransProR'. However, since 'ggraph' caused
                        frequent GitHub Action errors during the
                        creation of 'TransProR', the author directly
                        referenced the involved functions in
                        'TransProR'. This is not the author's original
                        creation. All users please be aware!
gene_color              Merge Genes with Color Information Based on
                        Up/Down Regulation
gene_highlights         Add gene highlights to a ggtree object
gene_map_pathway        Create Pathway-Gene Mapping Data Frame
get_gtex_exp            Get GTEx Expression Data for Specific Organ
get_tcga_exp            TCGA Expression Data Processing
gtree                   Phylogenetic Tree Object
highlight_genes         Add Highlights for Genes on a Phylogenetic Tree
limma_analyze           Differential Gene Expression Analysis using
                        limma and voom
log_transform           Log transformation decision and application on
                        data
merge_density_foldchange
                        Create high-density region plot with optional
                        points, density rugs, and contours
merge_gtex_tcga         Merge gene expression data from GTEx and TCGA
                        datasets
merge_id_position       Merge Data Frames by Common Row Names with
                        Additional Columns
merge_method_color      Merge Data Frames with Specific Method and
                        Color Columns
new_ggraph              Generate a graphical representation of pathway
                        gene maps
pathway_count           Count Genes Present in Pathways Above a
                        Threshold
pathway_description     Describe Genes Present in Selected Pathways
prep_deseq2             Prepare DESeq2 data for plotting
prep_edgeR              Prepare edgeR DEG data for plotting
prep_limma              Prepare limma-voom DEG data for plotting
prep_wilcoxon           Prepare Wilcoxon DEG data for plotting
process_heatdata        Process Heatmap Data with Various Selection
                        Options
seek_gtex_organ         Load and Process GTEX Phenotype Data to
                        Retrieve Primary Site Counts
selectPathways          Randomly Select Pathways with Limited Word
                        Count
spiral_newrle           Render a Spiral Plot Using Run-Length Encoding
stat_xspline            X-spline Statistic for ggplot2 (adapted from
                        ggalt)
