Package: RRNA 1.3

JP Bida

RRNA: Secondary Structure Plotting for RNA

Functions for creating and manipulating RNA secondary structure plots.

Authors:Jim Maher [ths], JP Bida [aut, cre], Jonathan Price [ctb]

RRNA_1.3.tar.gz
RRNA_1.3.zip(r-4.5)RRNA_1.3.zip(r-4.4)RRNA_1.3.zip(r-4.3)
RRNA_1.3.tgz(r-4.4-any)RRNA_1.3.tgz(r-4.3-any)
RRNA_1.3.tar.gz(r-4.5-noble)RRNA_1.3.tar.gz(r-4.4-noble)
RRNA_1.3.tgz(r-4.4-emscripten)RRNA_1.3.tgz(r-4.3-emscripten)
RRNA.pdf |RRNA.html✨
RRNA/json (API)
NEWS

# Install 'RRNA' in R:
install.packages('RRNA', repos = c('https://jlp-bioinf.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jlp-bioinf/rrna/issues

On CRAN:

4.33 score 1 stars 1 packages 47 scripts 294 downloads 26 exports 0 dependencies

Last updated 7 months agofrom:06185cb620. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:addBreaksalignCoordaptPlotCTbackwardbplfilecircleCoordcoord2compct2coordct2knetct2ssforwardgenCordsgenDBloadCoordsloadCtloopLengthmakeCtpairScorespseudoKnotRNAPlotrotateSrotateVstemCordstransformFoldtranslatevalidCT

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
RNA secondary structure plotingRRNA-package RRNA
Internal Function - labels RNA structures taken from PDB with gaps in nucleotide sequencesaddBreaks
Alignment of secondary structure folds to 2 nucleotides.alignCoord
RNA secondary structure plotting from CT filesaptPlotCT
Internal function for moving through secondary structuresbackward
Creates a bpl file from a coordinate filebplfile
Internal function for finding the coordinates of NT's in a circlecircleCoord
Generates secondary structure components from a coordinate filecoord2comp
Generate coordinate filect2coord
creates a knet file from a CT filect2knet
Generates secondary structure components from a coordinate filect2ss
Internal function for moving through secondary structuresforward
Generate components from hydrogen bond data extracted from a PDB file using RSIM.fuzzy2comp
Convert hydrogen bond data from RSIM 3D RNA structure into 2D secondary structuresfuzzy2ct
Internal function that generates coordinates for a given loop starting and stopping at p1 and p2 respectfullygenCords
Internal Function for creating component databasegenDB
Loads a coordinate file into a data frameloadCoords
Loads a CT file into an R data frameloadCt
internal function that determines the length of a looploopLength
make a CT file from a structure and sequencemakeCt
Identifies base-pairs from hydrogen bonding datapairScores
removes pseudoknots from a ct filepseudoKnot
Generic RNA Secondary Structure Plotting FunctionRNAPlot
Internal function to rotate a single pointrotateS
internal function to rotate a vector of pointsrotateV
internal function that generates coordinates for a stemstemCords
Internal function to translate and rotate a secondary structure plottransformFold
internal function for translating pointstranslate
Validate a CT FilevalidCT