DNAshapeR: High-throughput prediction of DNA shape features
Version 1.4.0

DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.

Browse man pages Browse package API and functions Browse package files

AuthorTsu-Pei Chiu and Federico Comoglio
Bioconductor views DNA3DStructure Software StructuralPrediction
Date of publicationNone
MaintainerTsu-Pei Chiu <tsupeich@usc.edu>
LicenseGPL-2
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DNAshapeR")

Man pages

DNAshapeR-package: DNAshapeR package for high-throughput prediction of DNA shape...
encodeKMerSeq: Encode k-mer DNA sequence features
encodeNstOrderShape: Encode n-st order shape features DNAshapeR can be used to...
encodeSeqShape: Encode k-mer DNA sequence and n-th order DNA Shape features
getFasta: Extract fasta sequence given a set of genomic intervals and a...
getShape: Predict DNA shape from a FASTA file
heatShape: Plot heatmap of DNA shape features
normalize: Min-Max normalization
normalizeShape: Normalize n-st order shape features
plotShape: Plot metaprofiles of DNA shape features
readShape: Read (parse) DNA shape predictions
trackShape: Plot track view of DNA shape features

Functions

DNAshapeR-package Man page
encodeKMerSeq Man page Source code
encodeNstOrderShape Man page Source code
encodeSeqShape Man page Source code
getDNAShape Source code
getFasta Man page Source code
getShape Man page Source code
heatShape Man page Source code
normalize Man page Source code
normalizeShape Man page Source code
plotShape Man page Source code
readShape Man page Source code
trackShape Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/core.R
R/encodeSeqShape.R
R/getFasta.R
R/getShape.R
R/plotShape.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/DNAshapeR.R
inst/doc/DNAshapeR.Rmd
inst/doc/DNAshapeR.html
inst/extdata
inst/extdata/CGRsample.fa
inst/extdata/CGRsample_short.fa
inst/extdata/SELEXsample.fa
inst/extdata/SELEXsample.s
inst/extdata/SELEXsample_short.fa
inst/extdata/SELEXsample_short.s
inst/extdata/SingleSeqsample.fa
inst/extdata/SingleSeqsample.fa.MGW
man
man/DNAshapeR-package.Rd
man/encodeKMerSeq.Rd
man/encodeNstOrderShape.Rd
man/encodeSeqShape.Rd
man/getFasta.Rd
man/getShape.Rd
man/heatShape.Rd
man/normalize.Rd
man/normalizeShape.Rd
man/plotShape.Rd
man/readShape.Rd
man/trackShape.Rd
src
src/OptionParser.cpp
src/OptionParser.h
src/Output.cpp
src/Output.h
src/RcppExports.cpp
src/ReadData.cpp
src/ReadData.h
src/SNP.cpp
src/SNP.h
src/ShapePrediction.cpp
src/TableCompiler.cpp
src/TableCompiler.h
src/common.h
src/map.cpp
src/map.h
src/prediction.cpp
src/prediction.h
src/properties.cpp
src/properties.h
src/utilities.cpp
src/utilities.h
tests
tests/testthat
tests/testthat.R
tests/testthat/test_read.R
vignettes
vignettes/DNAshapeR.Rmd
DNAshapeR documentation built on May 20, 2017, 10:29 p.m.