Function reference
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calculate_condition_mean_sd_per_gene() - Calculate statistics for each gene of an expression matrix given a grouping
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crossPanelUI()crossPanelServer() - Generate the cross plot panel of the shiny app
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cross_plot() - Create a cross plot comparing differential expression (DE) results
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DEanalysis_edger()DEanalysis_deseq2() - Perform differential expression (DE) analysis on an expression matrix
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DEpanelUI()DEpanelServer() - Generate the DE panel of the shiny app
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DEplotPanelUI()DEplotPanelServer() - Generate the DE plot plot panel of the shiny app
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DEsummaryPanelUI()DEsummaryPanelServer() - Generate the DE summary panel of the shiny app
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determine_uds() - Determine the pattern between two intervals
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enrichmentPanelUI()enrichmentPanelServer() - Generate the enrichment panel of the shiny app
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expression_heatmap() - Create heatmap of an expression matrix
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find_regulators_with_recurring_edges() - Find recurring regulators
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generateShinyApp() - Generate all files required for an autonomous shiny app
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get_link_list_rename() - Convert the adjacency matrix to network links
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GRNCisPanelUI()GRNCisPanelServer() - Generate the GRN cis integration panel of the shiny app
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GRNCustomPanelUI()GRNCustomPanelServer() - Generate the GRN custom integration panel of the shiny app
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GRNpanelUI()GRNpanelServer() - Generate the GRN panel of the shiny app
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GRNTransPanelUI()GRNTransPanelServer() - Generate the GRN trans integration panel of the shiny app
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infer_GRN() - Perform GRN inference
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jaccard_heatmap() - Create a heatmap of the Jaccard similarity index (JSI) between samples of an experiment
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jaccard_index() - Calculate the Jaccard similarity index (JSI) between two vectors
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landingPanelUI()landingPanelServer() - Generate the landing page panel of the shiny app
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make_heatmap_matrix() - Create a matrix of the average expression of each gene in each condition
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make_pattern_matrix() - Create a matrix of the patterns between conditions
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ma_plot()ma_enhance() - Create an MA plot visualising differential expression (DE) results
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modalityPanelUI()modalityPanelServer() - Generate an app panel for a modality
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noisyr_counts_with_plot() - Apply a modified noisyR counts pipeline printing a plot
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patternPanelUI()patternPanelServer() - Generate the expression patterns panel of the shiny app
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plot_GRN() - Plot a GRN
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plot_line_pattern() - Create a line plot of average expression across conditions
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plot_pca() - Create a principal component analysis (PCA) plot the samples of an experiment
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plot_upset() - Visualise the overlap of edges between different networks
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preprocessExpressionMatrix() - Pre-process the expression matrix before generating the shiny app
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preprocess_miRTarBase() - Creates a comparison table for miRTarBase to be used for custom integration
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QCpanelUI()QCpanelServer() - Generate the QC panel of the shiny app
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rescale_matrix() - Rescale a matrix
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sampleSelectPanelUI()sampleSelectPanelServer() - Generate the sample select panel of the shiny app
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volcano_plot()volcano_enhance() - Create a volcano plot visualising differential expression (DE) results