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

## Documentation for package ‘RNAprobR’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.