DNAshapeR: High-throughput prediction of DNA shape features

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DNAshapeR")
AuthorTsu-Pei Chiu and Federico Comoglio
Bioconductor views DNA3DStructure Software StructuralPrediction
Date of publicationNone
MaintainerTsu-Pei Chiu <tsupeich@usc.edu>
LicenseGPL-2
Version1.2.0

View on Bioconductor

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

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