An R package for analysis of massive parallel sequencing based RNA structure probing data

Documentation for package ‘RNAprobR’ version 1.8.0

bam2bedgraph	Function converts bam file to bedgraph by counting number of reads starting at each position (termination counts) It creates two-track bedgraph file (one track for each strand).
BED2txDb	Bedgraph to TranscriptDb object
bedgraph2norm	Import bedgraph to GRanges
comp	Arranging information from GRanges produced by readsamples() on per position (nucleotide) basis.
compdata	Create or extend norm_GR GRanges using Comp_GR GRanges
correct_oversaturation	Correcting EUC of oversaturated fragments.
dtcr	Calculate deltaTCR.
GR2norm_df	Export normalized GRanges object to data frame
k2n_calc	Calculate number of Estimated Unique Counts (EUC's) corresponding to given number of observed unique barcodes.
norm2bedgraph	Exporting data in norm_df data frame (product of dtcr, slograt and swinsor) to bedgraph format compatible with UCSC Genome Browser
norm_df2GR	Function to convert norm_df data frame (product of GR2norm_df()) to GRanges.
plotReads	Plotting ranges from GRanges
plotRNA	Plot normalized values over transcript positions
readsamples	Import of tables prepared by Galaxy workflow to R environment
slograt	Smooth Log2-ratio
swinsor	Smooth Winsorization
swinsor_vector	Smooth Winsor Normalization
winsor	Winsor normalization with fitting to <0,1> range.