nucleR is a R/Bioconductor package for working with tiling arrays and next generation sequencing. It uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and flexible nucleosome calling. More information is available in the article:
Oscar Flores and Modesto Orozco (2011). nucleR: a package for non-parametric nucleosome positioning. Bioinformatics 2011, doi:10.1093/bioinformatics/btr345
Most updated nucleR code and manual are available in the Bioconductor repository. This is included in the release version of Bioconductor since v.2.10.
Once nucleR is installed, you can check its main functions by executing the example workflow: