Man pages for noisyr
Noise Quantification in High Throughput Sequencing Output

calculate_expression_profileCalculate the expression profile of a gene
calculate_expression_similarity_countsCalcualate the expression levels and expression levels...
calculate_expression_similarity_transcriptCalcualte the distance matrices using the BAM files
calculate_first_minimum_densityFunction to find the first local minimum of the density of a...
calculate_noise_thresholdFunction to calculate the noise threshold for a given...
calculate_noise_threshold_method_statisticsFunction to tabulate statistics for different methods of...
cast_gtf_to_genesFunction to extract exon names and positions from a gtf file
cast_matrix_to_numericCast a matrix of any type to numeric
filter_genes_transcriptFunction to filter the gene table for the transcript approach
get_methods_calculate_noise_thresholdShow the methods for calculating a noise threshold
get_methods_correlation_distanceShow the methods for calculating correlation or distance
noisyrRun the noisyR pipeline
noisyr_countsRun the noisyR pipeline for the count matrix approach
noisyr_transcriptRun the noisyR pipeline for the transcript approach
optimise_window_lengthOptimise the elements per window for the count matrix...
plot_expression_similarityPlot the similarity against expression levels
remove_noise_from_bamsFunction to remove the noisy reads from the BAM files
remove_noise_from_matrixFunction to remove the noisy reads from the expression matrix
noisyr documentation built on April 16, 2021, 5:07 p.m.