correlogram_pheatmap    Function to create a correlogram pheatmap,
                        i.e., a plot to check randomness in the data
                        set.
diffExpr                Main wrapper for executing the entire pipeline
                        from reading in expression data such as count
                        files to producing text files and graphs
diff_expr_3d_scatterplot
                        Function to generate a 3D scatterplot
diff_expr_PCA           Function to do PCA using 'stats::prcomp'
diff_expr_PCA_ggbiplot
                        Function to generate a PCA biplot using
                        'ggbiplot.n', a version of 'ggbiplot' from
                        https://github.com/vqv/ggbiplot.
diff_expr_PCA_ggplot    Function to generate an ordinary
                        two-dimensional PCA plot using 'ggplot2'
diff_expr_QC_plots      Main wrapper function for QC plots
diff_expr_biomart       Function to retrieve additional information
                        from biomart
diff_expr_dendro_plot   Function to generate dendrogram plots based on
                        hierarchical clustering
diff_expr_extract_contrasts
                        Function to extract contrasts and generate top
                        tables and plots
diff_expr_filter_counts
                        Function to filter counts
diff_expr_fit           Function to compute linear model fit and
                        optionally apply 'voom' beforehand
diff_expr_get_samp_info
                        Function to standardize samp.info sample
                        information data frame
diff_expr_ggplot_mds    Function to generate a MDS plot using 'ggplot2'
diff_expr_ma_plot       Function to generate a M-A plot using 'ggplot2'
diff_expr_make_contrasts
                        Function to make contrast matrix
diff_expr_make_design   Function to create design matrix
diff_expr_mds_plot      Wrapper around 'limma::plotMDS' to generate a
                        MDS plot
diff_expr_pseudo_counts
                        Function to calculate pseudo counts
                        representing batch-corrected normalised but
                        untransformed values
diff_expr_pval_hist_plot
                        Function to generate a histogram of the P-Value
                        distribution
diff_expr_read_counts   Function to read counts as produced by
                        htseq-count
diff_expr_volcano_plot
                        Function to generate a Volcano plot using
                        'ggplot2'
diffr_expr_generate_cleaned_de_table_output
                        Helper function to generate an output table
                        with only most relevant columns
diffr_pheatmap          Function to create a heatmap from differential
                        gene expression values
diffr_venn              Function to produce a Venn diagram of
                        differentially expressed gene tables
diffwrap                Differential expression analysis of RNA-Seq
                        data
diffwrap_counts         Simulated RNA-Seq read counts for the package
                        examples
diffwrap_samp_info      Sample sheet accompanying the simulated example
                        counts
format_ensembl_ids_annotated_to_term
                        Helper function for formatting the gene ID
                        column of enrichment data frame.
get_hm_breaks           Function to define breaks to be used for
                        changing the palette of the heatmap.
get_hm_colors           Function to compute colour palettes to be used
                        in the heatmap.
ggbiplot.n              Make a biplot of PCA output data using ggplot2.
make_pheatmap_anno_color
                        Function to create the annotation colour list
                        used in the heatmap
pheatmap_plots          Function to generate heatmap of gene expression
                        values
plot_enrichment_network
                        Function for making network visualisation based
                        on enrichment result, DE gene table and
                        thresholding. Can take the input tables either
                        as data frames or Excel files
prepare_scale_for_legend
                        Helper function for enrichment visualisations:
                        prepare plot legend y coordinates and labels
prepare_volcano_of_given_property
                        Helper function that returns a volcano plot.
quantile_breaks         Function to define quantile breaks to be used
                        for changing the palette of the heatmap.
reorderFactors          Function which reorders the levels of a column
                        of a data frame specified as a factor
run.topGO               Function to run GO term enrichment analysis
                        using the 'topGO' package.
runEnrichmentAnalyses   Wrapper for executing various enrichment
                        analyses
run_clusterProfiler_GO
                        Runs clusterProfiler GO enrichment function for
                        a DEG list or for a ranked gene list.
run_clusterProfiler_KEGG
                        Runs clusterProfiler KEGG enrichment function
                        for a DEG list or for a ranked gene list.
run_gprofiler           Runs gprofiler function for a DEG list or for a
                        ranked gene list.
