Poly(A) Tail Length Estimator for Oxford Nanopore RNA and DNA Reads

Documentation for package ‘tailfindr’ version 1.3

annotate_tails	Assign transcript IDs to poly(A) tails
explore_basecaller_and_fast5type	Explore a fast5 file to find parameters of the experiment
extract_read_data	Extract the read data from a fast5 file
extract_sequence_between_boundaries	Extract sequence between two samples boundaries
find_dna_tailtype	Finds if a DNA read is poly(A) read or poly(T) read
find_dna_tail_per_read	Find poly(A)/poly(T) tail in a single DNA read
find_rna_polya_crude_start_end	Find the crude start and end of polyA tail in RNA read
find_rna_polya_precise_start_end	Finds the precise RNA tail and start
find_rna_polya_tail_per_read	Find Poly(A) tail in a single RNA read.
find_sample_index_for_fastq_base	Finds raw data sample index corresponding to a base.
find_tails	Estimates poly(A)/(T) tail lengths in Oxford Nanopore RNA and DNA reads
get_custom_fp_ep	Get custom front and end primers from optional parameters list
get_dna_datatype	Parse optional params to get the type of DNA
left_to_right_sliding_window_dna	Sliding window from left to right
left_to_right_sliding_window_rna	Sliding window from left to right
read_sam	Read SAM file Author credits: Grischa Toedt & VladaMilch
rectify	Convert negative values in the signal to corresponding positive values.
right_to_left_sliding_window_dna	Sliding window from right to left.
right_to_left_sliding_window_rna	Sliding window from right to left.
smoothen_rle_intersections_rna	Smoothen RLE intersections for RNA
truncate_spikes	Truncate spikes
z_normalize	z-normalize