# An R package for RNA visualization and analysis

## Documentation for package ‘R4RNA’ version 1.35.0

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

## Help Pages

R4RNA-package | An R package for RNA visualization and analysis
alignmentCanonical | Compute statistics for a multiple sequence alignments
alignmentConservation | Compute statistics for a multiple sequence alignments
alignmentCovariation | Compute statistics for a multiple sequence alignments
alignmentPercentGaps | Compute statistics for a multiple sequence alignments
as.helix | Coerce to a Helix Data Frame
baseConservation | Compute statistics for a multiple sequence alignments
basepairCanonical | Compute statistics for a multiple sequence alignments
basepairConservation | Compute statistics for a multiple sequence alignments
basepairCovariation | Compute statistics for a multiple sequence alignments
basepairFrequency | Calculates the frequency of each basepair
blankPlot | Create a blank plotting canvas
collapseHelix | Expand or collapse helices to and from basepairs
colourByBasepairFrequency | Assign colours to helices
colourByCanonical | Assign colours to helices
colourByConservation | Assign colours to helices
colourByCount | Assign colours to helices
colourByCovariation | Assign colours to helices
colourByUnknottedGroups | Assign colours to helices
colourByValue | Assign colours to helices
defaultPalette | Assign colours to helices
expandHelix | Expand or collapse helices to and from basepairs
fasta | Helices predicted by TRANSAT with p-values
helix | Helices predicted by TRANSAT with p-values
helixCanonical | Compute statistics for a multiple sequence alignments
helixConservation | Compute statistics for a multiple sequence alignments
helixCovariation | Compute statistics for a multiple sequence alignments
helixToBpseq | Convert helix structures to and from other formats
helixToConnect | Convert helix structures to and from other formats
helixToVienna | Convert helix structures to and from other formats
is.helix | Coerce to a Helix Data Frame
isConflictingHelix | Logical filters of helix by type
isDuplicatingHelix | Logical filters of helix by type
isOverlappingHelix | Logical filters of helix by type
known | Helices predicted by TRANSAT with p-values
logceiling | Log base 10 sequence, floor and ceiling
logfloor | Log base 10 sequence, floor and ceiling
logseq | Log base 10 sequence, floor and ceiling
maxHeight | Create a blank plotting canvas
parseBracket | Coerce to a Helix Data Frame
plotArc | Plots helices in arc diagram
plotArcs | Plots helices in arc diagram
plotCovariance | Plot nucleotide sequence coloured by covariance
plotDoubleCovariance | Plot nucleotide sequence coloured by covariance
plotDoubleHelix | Plots helices in arc diagram
plotHelix | Plots helices in arc diagram
plotOverlapCovariance | Plot nucleotide sequence coloured by covariance
plotOverlapHelix | Plots helices in arc diagram
R4RNA | An R package for RNA visualization and analysis
readBpseq | Read secondary structure file
readConnect | Read secondary structure file
readHelix | Read secondary structure file
readVienna | Read secondary structure file
structureMismatchScore | Scores how a basepair structure fits a sequence
unknottedGroups | Partition basepairs into unknotted groups
viennaToHelix | Convert helix structures to and from other formats
writeHelix | Write out a helix data frame into a text file