calculate_expression_profile
                        Calculate the expression profile of a gene
calculate_expression_similarity_counts
                        Calcualate the expression levels and expression
                        levels similarity matrices using the count
                        matrix
calculate_expression_similarity_transcript
                        Calcualte the distance matrices using the BAM
                        files
calculate_first_minimum_density
                        Function to find the first local minimum of the
                        density of a vector
calculate_noise_threshold
                        Function to calculate the noise threshold for a
                        given expression matrix and parameters
calculate_noise_threshold_method_statistics
                        Function to tabulate statistics for different
                        methods of calculating the noise threshold
cast_gtf_to_genes       Function to extract exon names and positions
                        from a gtf file
cast_matrix_to_numeric
                        Cast a matrix of any type to numeric
filter_genes_transcript
                        Function to filter the gene table for the
                        transcript approach
get_methods_calculate_noise_threshold
                        Show the methods for calculating a noise
                        threshold
get_methods_correlation_distance
                        Show the methods for calculating correlation or
                        distance
noisyr                  Run the noisyR pipeline
noisyr_counts           Run the noisyR pipeline for the count matrix
                        approach
noisyr_transcript       Run the noisyR pipeline for the transcript
                        approach
optimise_window_length
                        Optimise the elements per window for the count
                        matrix approach
plot_expression_similarity
                        Plot the similarity against expression levels
remove_noise_from_bams
                        Function to remove the noisy reads from the BAM
                        files
remove_noise_from_matrix
                        Function to remove the noisy reads from the
                        expression matrix
