Learn R Programming

RNAprobR (version 1.4.0)

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

Description

This package facilitates analysis of Next Generation Sequencing data for which positional information with a single nucleotide resolution is a key. It allows for applying different types of relevant normalizations, data visualization and export in a table or UCSC compatible bedgraph file.

Copy Link

Version

Version

1.4.0

License

GPL (>=2)

Maintainer

Nikos Sidiropoulos

Last Published

February 15th, 2017

Functions in RNAprobR (1.4.0)

norm2bedgraph

Exporting data in norm_df data frame (product of dtcr, slograt and swinsor) to bedgraph format compatible with UCSC Genome Browser
swinsor_vector

Smooth Winsor Normalization
k2n_calc

Calculate number of Estimated Unique Counts (EUC's) corresponding to given number of observed unique barcodes.
dtcr

Calculate deltaTCR.
plotReads

Plotting ranges from GRanges
plotRNA

Plot normalized values over transcript positions
winsor

Winsor normalization with fitting to <0,1> range.
swinsor

Smooth Winsorization
bedgraph2norm

Import bedgraph to GRanges
BED2txDb

Bedgraph to TranscriptDb object
comp

Arranging information from GRanges produced by readsamples() on per position (nucleotide) basis.
readsamples

Import of tables prepared by Galaxy workflow to R environment
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).
norm_df2GR

Function to convert norm_df data frame (product of GR2norm_df()) to GRanges.
correct_oversaturation

Correcting EUC of oversaturated fragments.
compdata

Create or extend norm_GR GRanges using Comp_GR GRanges
GR2norm_df

Export normalized GRanges object to data frame
slograt

Smooth Log2-ratio