Package: R4RNA 1.35.0
Daniel Lai
R4RNA: An R package for RNA visualization and analysis
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.
Authors:
R4RNA_1.35.0.tar.gz
R4RNA_1.35.0.zip(r-4.5)R4RNA_1.35.0.zip(r-4.4)R4RNA_1.35.0.zip(r-4.3)
R4RNA_1.35.0.tgz(r-4.4-any)R4RNA_1.35.0.tgz(r-4.3-any)
R4RNA_1.35.0.tar.gz(r-4.5-noble)R4RNA_1.35.0.tar.gz(r-4.4-noble)
R4RNA_1.35.0.tgz(r-4.4-emscripten)R4RNA_1.35.0.tgz(r-4.3-emscripten)
R4RNA.pdf |R4RNA.html✨
R4RNA/json (API)
NEWS
| # Install 'R4RNA' in R: |
| install.packages('R4RNA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:R4RNA-1.35.0(bioc 3.21)R4RNA-1.34.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
alignmentmultiplesequencealignmentpreprocessingvisualizationdataimportdatarepresentationmultiplecomparison
Last updated 2 months agofrom:50cd94f535. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 04 2024 |
| R-4.5-win | NOTE | Dec 04 2024 |
| R-4.5-linux | NOTE | Dec 04 2024 |
| R-4.4-win | NOTE | Dec 04 2024 |
| R-4.4-mac | NOTE | Dec 04 2024 |
| R-4.3-win | NOTE | Dec 04 2024 |
| R-4.3-mac | NOTE | Dec 04 2024 |
Exports:alignmentCanonicalalignmentConservationalignmentCovariationalignmentPercentGapsas.helixbaseConservationbasepairCanonicalbasepairConservationbasepairCovariationbasepairFrequencyblankPlotcollapseHelixcolourByBasepairFrequencycolourByCanonicalcolourByConservationcolourByCountcolourByCovariationcolourByUnknottedGroupscolourByValuedefaultPaletteexpandHelixhelixCanonicalhelixConservationhelixCovariationhelixToBpseqhelixToConnecthelixToViennais.helixisConflictingHelixisDuplicatingHelixisOverlappingHelixlogceilinglogfloorlogseqmaxHeightplotArcplotArcsplotCovarianceplotDoubleCovarianceplotDoubleHelixplotHelixplotOverlapCovarianceplotOverlapHelixreadBpseqreadConnectreadHelixreadViennastructureMismatchScoreunknottedGroupsviennaToHelixwriteHelix
Dependencies:askpassBiocGenericsBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| An R package for RNA visualization and analysis | R4RNA-package R4RNA |
| Compute statistics for a multiple sequence alignments | alignmentCanonical alignmentConservation alignmentCovariation alignmentPercentGaps baseConservation basepairCanonical basepairConservation basepairCovariation helixCanonical helixConservation helixCovariation |
| Calculates the frequency of each basepair | basepairFrequency |
| Expand or collapse helices to and from basepairs | collapseHelix expandHelix |
| Coerce to a Helix Data Frame | as.helix is.helix parseBracket |
| Assign colours to helices | colourByBasepairFrequency colourByCanonical colourByConservation colourByCount colourByCovariation colourByUnknottedGroups colourByValue defaultPalette |
| Convert helix structures to and from other formats | helixToBpseq helixToConnect helixToVienna viennaToHelix |
| Plot nucleotide sequence coloured by covariance | plotCovariance plotDoubleCovariance plotOverlapCovariance |
| Create a blank plotting canvas | blankPlot maxHeight |
| Helices predicted by TRANSAT with p-values | fasta helix known |
| Partition basepairs into unknotted groups | unknottedGroups |
| Logical filters of helix by type | isConflictingHelix isDuplicatingHelix isOverlappingHelix |
| Log base 10 sequence, floor and ceiling | logceiling logfloor logseq |
| Plots helices in arc diagram | plotArc plotArcs plotDoubleHelix plotHelix plotOverlapHelix |
| Read secondary structure file | readBpseq readConnect readHelix readVienna |
| Scores how a basepair structure fits a sequence | structureMismatchScore |
| Write out a helix data frame into a text file | writeHelix |