Scripts and wrappers to run nucleR and NucleosomeDynamics on the backend of a server
Primary data Score: Stiffness estimation. It's the energy required to move the nucleosome (expressed in cal/bp), it's derived from the gaussian standard deviation.
Attributes nucleR_score: the nucleR score given to that nucleosome nucleR.class: the nucleR class given to that nucleosome gauss_k: the height of the peak of the gaussian curve gauss_m: the position of the peak of the gaussian curve gauss_sd: the standard deviation of the gaussian curve
Primary data Position: region where the movement happens Type: change in the nucleosome map Score: magnitude of the change
Attributes class: type of hotspot (see help for all possible types) nuc: to which nucleosome the movement belongs. NA means that the hostpot couldn't be unequivocally associated to one nucleosome. number_of_reads: number of reads involved in this movement hreads: number of reads involved in the movement relative to the number of reads present in the area. This value ranges from 0 to 1 and the closest it is to 1, the more significant the movement.
Primary data Score: Positionning score. It is calculated as the weighted sum of width and height scores.
Attributes score_width: Witdth score. It is a measure of how sharp a peak is. A value of 0 would be an extremely wide peak and a value of 1 a very sharp one. score_height: Height score. Tells how large a peak of a nucleosome is. The bigger this number, the higher the peak. class: Whether the nucleosome is well-positioned (W) or fuzzy (F) or undetermined. The taken value depends on score_h and score_w. Undetermined means the exact position of the nucleosome cannot be determined due to strong fuzziness.
Attributes nucleosome_first: First nucleosome of the gene. nucleosme_last: Last nucleosome of the gene. score_phase: Is a measure of the phase between the first and the last nucleosome. A score of 0 means the nucleosome are completely phased and a score of 82 corresponds to totally antiphased nucleosomes. score_autocorrelation: It is directly computed from the experimental coverage and is quantitative measure of the periodicity of nucleosomes inside the gene body.
Primary data Position: Region between two nucleosomes surrounding the TSS.
Attributes classification: Descriptor of the Transcription Start Site. See the help for possible options. distance: Distance in base pairs between the nucleosome +1 and the nucleosome -1. id nucleosome minus1: Position of the nucleosome -1. nucleosome plus1: Position of the nucleosome +1 TTS_position: Position of the Transcription Start Site.