VISTA-accessors         Accessor Methods for VISTA Object
VISTA-class             VISTA S4 Class Definition
as_vista                Coerce SummarizedExperiment to VISTA
benchmark_vista_equivalence
                        Benchmark VISTA against standalone
                        differential-expression backends
count_data              Example RNA-seq count matrix shipped with VISTA
create_vista            Create a VISTA Object with Internal DE Analysis
derive_vista_metadata   Derive starter sample metadata from count
                        sample names
enrichMsigDB            Perform MSigDB over-representation analysis on
                        a VISTA object
example_vista           Build a small example VISTA object
export_vista_assets     Export a complete VISTA asset bundle
get_cell_fractions      Retrieve stored cell fraction estimates
get_celltype_barplot    Plot cell-type composition as stacked bars
get_celltype_group_dotplot
                        Plot group-level deconvolution scores as dot
                        plot
get_celltype_heatmap    Plot cell-type deconvolution heatmap
get_corr_heatmap        Draw a sample correlation heatmap
get_deg_alluvial        Plot alluvial diagram showing gene regulation
                        transitions across comparisons
get_deg_count_barplot   Barplot of DEG counts (Up/Down) across
                        comparisons
get_deg_count_donutplot
                        Donut chart of DEG counts (Up/Down) across
                        comparisons
get_deg_count_pieplot   Pie chart of DEG counts (Up/Down) across
                        comparisons
get_deg_venn_diagram    DEG Venn diagram
get_enrichment_chord    Chord diagram of enrichment gene-pathway
                        relationships
get_enrichment_plot     Plot enrichment results using -log10(FDR)
get_expression_barplot
                        Plot gene expression as barplots
get_expression_boxplot
                        Plot gene expression distributions as boxplots
get_expression_chromosome_plot
                        Chromosome plot for expression
get_expression_density
                        Plot expression distributions as density curves
get_expression_heatmap
                        Expression heatmap
get_expression_joyplot
                        Plot expression distributions as ridgelines
get_expression_lineplot
                        Gene expression line plot
get_expression_lollipop
                        Plot expression as a lollipop chart
get_expression_matrix   Retrieve an expression matrix from a VISTA
                        object
get_expression_raincloud
                        Raincloud plot of expression values
get_expression_scatter
                        Compare normalized expression between two
                        samples or groups
get_expression_violinplot
                        Violin plot of expression values
get_foldchange_barplot
                        Plot fold-change barplots across comparisons
                        for selected genes
get_foldchange_boxplot
                        Plot fold-change distributions across
                        comparisons
get_foldchange_chromosome_plot
                        Chromosome plot for fold change
get_foldchange_heatmap
                        Fold-change heatmap
get_foldchange_lineplot
                        Fold-change line plot across comparisons
get_foldchange_lollipop
                        Fold-change plotting helpers (overview)
get_foldchange_matrix   Extract a log2 fold-change matrix
get_foldchange_raincloud
                        Raincloud plot of fold-change distributions
                        across comparisons
get_foldchange_scatter
                        Fold-change scatterplot between two comparisons
get_genes_by_regulation
                        Get Genes by Regulation
get_go_enrichment       Run GO enrichment directly from a VISTA
                        comparison
get_gsea                Gene set enrichment analysis (GSEA) from a
                        VISTA comparison
get_kegg_enrichment     Run KEGG enrichment directly from a VISTA
                        comparison
get_ma_plot             Generate MA plot from a VISTA object
get_mds_plot            Generate an MDS plot for samples in a VISTA
                        object
get_msigdb_enrichment   Run MSigDB enrichment directly from a VISTA
                        comparison
get_pairwise_corr_plot
                        Plot pairwise correlations between samples
get_pathway_genes       Extract genes from enriched pathways
get_pathway_heatmap     Plot pathway-specific expression heatmaps from
                        enrichment output
get_pca_plot            PCA plot
get_umap_plot           Generate a UMAP plot for samples in a VISTA
                        object
get_volcano_plot        Generate a volcano plot for a comparison in a
                        VISTA object
match_vista_inputs      Match count and metadata inputs for VISTA
print.VISTA             Print a VISTA object like a
                        SummarizedExperiment
read_vista_counts       Read and standardize count inputs for VISTA
read_vista_metadata     Read and standardize sample metadata for VISTA
run_cell_deconvolution
                        Run Cell Deconvolution on Bulk RNA-seq from
                        VISTA Object
run_deseq_analysis      Run Differential Expression Analysis with
                        DESeq2, edgeR, or limma-voom
run_vista_report        Generate a publication-ready VISTA workflow
                        report
sample_metadata         Sample metadata accompanying the VISTA airway
                        example counts
save_vista_data         Save VISTA tabular outputs to disk
save_vista_plot         Save a VISTA plot object to disk
set_de_source           Set active DE source in a VISTA object
set_rowdata             Set or append rowData annotations on a VISTA
                        object
set_vista_comparison_colors
                        Set manual comparison colors in a VISTA object
set_vista_group_colors
                        Set manual group colors in a VISTA object
validate_vista          Validate a VISTA object
validate_vista_deep     Deep validation of VISTA
                        differential-expression fidelity
