Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning
Nucleosome Dynamics package offers a set of tools to analyze nucleosome positioning from MNase-seq experimental data and to compare experiments accounting for the transient and dynamic nature of nucleosomes under different cellular states. The programs are written in R, but additionally other implementations are available including two web-based platforms (MuGVRE and Galaxy) and two containerized installations (docker and singularity).
Buitrago D, Codo L, Illa R, de Jorge P, Battistini F, Flores O, Bayarri G, Royo R, Del Pino M, Heath S, Hospital A, Gelpi JL, Heath IB, Orozco M.
Nucleic Acids Res 2019 Oct; 47: 9511.
We 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.
PubMed: 31504766. Doi: 10.1093/nar/gkz759. OPEN Free PMC
Additional Information
The Nucleosome Dynamics server is available online with tools to analyze nucleosome positioning and compare experiments under different cellular states.
