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 |