Man pages for noisyr
Noise Quantification in High Throughput Sequencing Output
| calculate_expression_profile | Calculate the expression profile of a gene |
| calculate_expression_similarity_counts | Calcualate the expression levels and expression levels... |
| 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... |
| calculate_noise_threshold | Function to calculate the noise threshold for a given... |
| calculate_noise_threshold_method_statistics | Function to tabulate statistics for different methods of... |
| 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... |
| 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 |
