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 and Wang et al 2008. The core of the package was written in Fortran. Three functions including predNuPoP, readNuPoP, and plotNuPoP are provided for nucleosome positioning prediction, prediction results readin, and prediction results visualization respectively. The input DNA sequence can be of any length.
plotNuPoP
(Package: NuPoP) :
R function for plotting the predicted nucleosome positioning map and nucleosome occupancy map
This function produces two plots from a specified region based on the prediction results from function predNuPoP. The first plot is the nucleosome occupancy (grey color). In the second plot, in addition to the occupancy, Viterbi prediction (red rectangle) and the posterior probability for a position to be the start of a nucleosome (blue color) are superimposed.
predNuPoP
(Package: NuPoP) :
R function for nucleosome positioning prediction, occupancy score and nucleosome binding affinity score calculation
This function invokes Fortran codes to compute the Viterbi prediction of nucleosome positioning, nucleosome occupancy score and nucleosome binding affinity score . A pre-trained linker DNA length distribution for the current species is used in a duration Hidden Markov model.
providing 
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