DEanalysis              Perform differential expression (DE) analysis
                        on an expression matrix
DEpanel                 Generate the DE panel of the shiny app
DEplotPanel             Generate the DE plot plot panel of the shiny
                        app
DEsummaryPanel          Generate the DE summary panel of the shiny app
GRNCisPanel             Generate the GRN cis integration panel of the
                        shiny app
GRNCustomPanel          Generate the GRN custom integration panel of
                        the shiny app
GRNTransPanel           Generate the GRN trans integration panel of the
                        shiny app
GRNpanel                Generate the GRN panel of the shiny app
QCpanel                 Generate the QC panel of the shiny app
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
cross_plot              Create a cross plot comparing differential
                        expression (DE) results
determine_uds           Determine the pattern between two intervals
enrichmentPanel         Generate the enrichment panel of the shiny app
expression_heatmap      Create heatmap of an expression matrix
find_regulators_with_recurring_edges
                        Find recurring regulators
generateShinyApp        Generate all files required for an autonomous
                        shiny app
genes_barplot           Create a bar plot of expression for selected
                        genes across samples in an experiment
get_link_list_rename    Convert the adjacency matrix to network links
infer_GRN               Perform GRN inference
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
landingPanel            Generate the landing page panel of the shiny
                        app
ma_plot                 Create an MA plot visualising differential
                        expression (DE) results
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
modalityPanel           Generate an app panel for a modality
noisyr_counts_with_plot
                        Apply a modified noisyR counts pipeline
                        printing a plot
patternPanel            Generate the expression patterns panel of the
                        shiny app
plot_GRN                Plot a GRN
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
plot_upset              Visualise the overlap of edges between
                        different networks
preprocessExpressionMatrix
                        Pre-process the expression matrix before
                        generating the shiny app
preprocess_miRTarBase   Creates a comparison table for miRTarBase to be
                        used for custom integration
qc_density_plot         Create a density plot of log2 expression across
                        samples of an experiment
qc_violin_plot          Create a violin/box plot of expression across
                        samples of an experiment
rescale_matrix          Rescale a matrix
sampleSelectPanel       Generate the sample select panel of the shiny
                        app
scatter_plot            Create a scatter plot of expression between two
                        samples of an experiment
volcano_plot            Create a volcano plot visualising differential
                        expression (DE) results
