Buitrago, DianaCodó, LaiaIlla, RicardJorge, Pau deBattistini, FedericaFlores, OscarBayarri, GenisRoyo, RominaPino, Marc delHeath, SimonHospital, AdamGelpí, Josep LluísBrun-Heath, IsabelleOrozco, Modesto2020-04-062020-04-062019Buitrago D, Codó L, Illa R, de Jorge P, Battistini F, Flores O, Bayarri G, Royo R, Del Pino M, Heath S, Hospital A, Gelpí JL, Heath IB, Orozco M. Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning. Nucleic Acids Res. 2019; 47(18):9511-23. DOI: 10.1093/nar/gkz7590305-1048http://hdl.handle.net/10230/44159We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.application/pdfeng© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.cominfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/nar/gkz759Computational methodsChromatin and epigeneticsGenomicsinfo:eu-repo/semantics/openAccess