|
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 |