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.

Author
Tsu-Pei Chiu and Federico Comoglio
Date of publication
None
Maintainer
Tsu-Pei Chiu <tsupeich@usc.edu>
License
GPL-2
Version
1.2.0

View on Bioconductor

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

Files in this package

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