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R4RNA (version 1.0.0)

An R package for RNA visualization and analysis

Description

A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.

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Version

Version

1.0.0

License

GPL-3

Maintainer

Last Published

February 15th, 2017

Functions in R4RNA (1.0.0)

Find Unknotted Groups

Partition basepairs into unknotted groups
R4RNA-package

An R package for RNA visualization and analysis
Convert Helix Formats

Convert helix structures to and from other formats
Log10 Space Operations

Log base 10 sequence, floor and ceiling
Alignment Statistics

Compute statistics for a multiple sequence alignments
Coerce to Helix

Coerce to a Helix Data Frame
Basepair/Helix Conversion

Expand or collapse helices to and from basepairs
Example Data

Helices predicted by TRANSAT with p-values
Colour Helices

Assign colours to helices
Covariation Plots

Plot nucleotide sequence coloured by covariance
Read Structure File

Read secondary structure file
Structure Mismatch Score

Scores how a basepair structure fits a sequence
Basepair Frequency

Calculates the frequency of each basepair
Helix Type Filters

Logical filters of helix by type
Create Blank Plot

Create a blank plotting canvas
Write Helix

Write out a helix data frame into a text file
Plot Helix Structures

Plots helices in arc diagram