NuPoP: An R package for nucleosome positioning prediction

NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at http://nucleosome.stats.northwestern.edu.

Author
Ji-Ping Wang <jzwang@northwestern.edu>; Liqun Xi <lxi700@northwestern.edu>
Date of publication
None
Maintainer
Ji-Ping Wang<jzwang@northwestern.edu>
License
GPL-2
Version
1.24.0

View on Bioconductor

Man pages

NuPoP-package
An R package for nucleosome positioning prediction
plotNuPoP
R function for plotting the predicted nucleosome positioning...
predNuPoP
R function for nucleosome positioning prediction, occupancy...
readNuPoP
R function for plotting the predicted nucleosome positioning...

Files in this package

NuPoP/DESCRIPTION
NuPoP/NAMESPACE
NuPoP/R
NuPoP/R/plotNuPoP.R
NuPoP/R/predNuPoP.R
NuPoP/R/readNuPoP.R
NuPoP/R/sysdata.rda
NuPoP/build
NuPoP/build/vignette.rds
NuPoP/inst
NuPoP/inst/doc
NuPoP/inst/doc/NuPoP-intro.R
NuPoP/inst/doc/NuPoP-intro.Rnw
NuPoP/inst/doc/NuPoP-intro.pdf
NuPoP/inst/extdata
NuPoP/inst/extdata/test.seq
NuPoP/inst/extdata/test.seq_Prediction4.txt
NuPoP/man
NuPoP/man/NuPoP-package.Rd
NuPoP/man/plotNuPoP.Rd
NuPoP/man/predNuPoP.Rd
NuPoP/man/readNuPoP.Rd
NuPoP/src
NuPoP/src/vtbfb.f90
NuPoP/src/vtbfbNL4.f90
NuPoP/vignettes
NuPoP/vignettes/NuPoP-intro.Rnw
NuPoP/vignettes/NuPoP-manual.pdf