Interactive Shiny App for Bulk Sequencing Data

calculate_condition_mean_sd_per_gene Calculate statistics for each gene of an expression matrix given a grouping crossPanel Generate the cross plot panel of the shiny app crossPanelServer Generate the cross plot panel of the shiny app crossPanelUI Generate the cross plot panel of the shiny app cross_plot Create a cross plot comparing differential expression (DE) results DEanalysis Perform differential expression (DE) analysis on an expression matrix DEanalysis_deseq2 Perform differential expression (DE) analysis on an expression matrix DEanalysis_edger Perform differential expression (DE) analysis on an expression matrix DEpanel Generate the DE panel of the shiny app DEpanelServer Generate the DE panel of the shiny app DEpanelUI Generate the DE panel of the shiny app DEplotPanel Generate the DE plot plot panel of the shiny app DEplotPanelServer Generate the DE plot plot panel of the shiny app DEplotPanelUI Generate the DE plot plot panel of the shiny app DEsummaryPanel Generate the DE summary panel of the shiny app DEsummaryPanelServer Generate the DE summary panel of the shiny app DEsummaryPanelUI Generate the DE summary panel of the shiny app determine_uds Determine the pattern between two intervals enrichmentPanel Generate the enrichment panel of the shiny app enrichmentPanelServer Generate the enrichment panel of the shiny app enrichmentPanelUI Generate the enrichment panel of the shiny app expression_heatmap Create heatmap of an expression matrix generateShinyApp Generate all files required for an autonomous shiny app GRNpanel Generate the GRN panel of the shiny app GRNpanelServer Generate the GRN panel of the shiny app GRNpanelUI Generate the GRN panel of the shiny app jaccard_heatmap Create a heatmap of the Jaccard similarity index (JSI) between samples of an experiment jaccard_index Calculate the Jaccard similarity index (JSI) between two vectors make_heatmap_matrix Create a matrix of the average expression of each gene in each condition make_pattern_matrix Create a matrix of the patterns between conditions ma_enhance Create an MA plot visualising differential expression (DE) results ma_plot Create an MA plot visualising differential expression (DE) results noisyr_counts_with_plot Apply a modified noisyR counts pipeline printing a plot patternPanel Generate the expression patterns panel of the shiny app patternPanelServer Generate the expression patterns panel of the shiny app patternPanelUI Generate the expression patterns panel of the shiny app plot_line_pattern Create a line plot of average expression across conditions plot_pca Create a principal component analysis (PCA) plot the samples of an experiment preprocessExpressionMatrix Pre-process the expression matrix before generating the shiny app QCpanel Generate the QC panel of the shiny app QCpanelServer Generate the QC panel of the shiny app QCpanelUI Generate the QC panel of the shiny app rescale_matrix Rescale a matrix sampleSelectPanel Generate the sample select panel of the shiny app sampleSelectPanelServer Generate the sample select panel of the shiny app sampleSelectPanelUI Generate the sample select panel of the shiny app volcano_enhance Create a volcano plot visualising differential expression (DE) results volcano_plot Create a volcano plot visualising differential expression (DE) results

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