An R package for RNA visualization and analysis


[Up] [Top]

Documentation for package ‘R4RNA’ version 1.32.0

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