RRNA: Secondary Structure Plotting for RNA

Functions for creating and manipulating RNA secondary structure plots.

Author
JP Bida
Date of publication
2015-07-29 06:21:35
Maintainer
JP Bida <bida.john@gmail.com>
License
GPL-3
Version
1.0

View on CRAN

Man pages

alignCoord
Alignment of secondary structure folds to 2 nucleotides.
aptPlotCT
RNA secondary structure plotting from CT files
backward
Internal function for moving through secondary structures
bplfile
Creates a bpl file from a coordinate file
circleCoord
Internal function for finding the coordinates of NT's in a...
ct2coord
Generate coordinate file
ct2knet
creates a knet file from a CT file
forward
Internal function for moving through secondary structures
genCords
Internal function that generates coordinates for a given loop...
loadCoords
Loads a coordinate file into a data frame
loadCt
Loads a CT file into an R data frame
loopLength
internal function that determines the length of a loop
makeCt
make a CT file from a structure and sequence
pseudoKnot
removes pseudoknots from a ct file
RNAPlot
Generic RNA Secondary Structure Plotting Function
rotateS
Internal function to rotate a single point
rotateV
internal function to rotate a vector of points
RRNA-package
RNA secondary structure ploting
stemCords
internal function that generates coordinates for a stem
transformFold
Internal function to translate and rotate a secondary...
translate
internal function for translating points

Files in this package

RRNA
RRNA/inst
RRNA/inst/CITATION
RRNA/NAMESPACE
RRNA/R
RRNA/R/RRNA.r
RRNA/MD5
RRNA/DESCRIPTION
RRNA/man
RRNA/man/makeCt.Rd
RRNA/man/bplfile.Rd
RRNA/man/forward.Rd
RRNA/man/circleCoord.Rd
RRNA/man/ct2coord.Rd
RRNA/man/loopLength.Rd
RRNA/man/backward.Rd
RRNA/man/stemCords.Rd
RRNA/man/loadCoords.Rd
RRNA/man/aptPlotCT.Rd
RRNA/man/loadCt.Rd
RRNA/man/genCords.Rd
RRNA/man/RNAPlot.Rd
RRNA/man/RRNA-package.Rd
RRNA/man/translate.Rd
RRNA/man/alignCoord.Rd
RRNA/man/ct2knet.Rd
RRNA/man/pseudoKnot.Rd
RRNA/man/rotateV.Rd
RRNA/man/rotateS.Rd
RRNA/man/transformFold.Rd