| 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 |