Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos

BMC Bioinformatics

Table 1 Functions of the software packages used in this study

NuPoP [16]	nuCpos	Description
predNuPoP*	predNuCpos**	Prediction of nucleosome positioning based on dHMMs
readNuPoP		Loading of prediction results
plotNuPoP		Plotting of prediction results
	HBA	Calculation of HBA scores
	localHBA	Calculation of local HBA scores
	mutNuCpos	Prediction of the effects of genetic alterations on nucleosome positioning

*MNase-seq-based. HBA scores are smoothed before outputting the prediction results
**Chemical map-based. Smoothing of HBA scores is optional

ISSN: 1471-2105