BED2txDb                Bedgraph to TranscriptDb object
GR2norm_df              Export normalized GRanges object to data frame
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).
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.
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.
plotRNA                 Plot normalized values over transcript
                        positions
plotReads               Plotting ranges from GRanges
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.
