Nucleosome positioning software tools | ATAC sequencing data analysis
Nucleosomal patterns result from the combined contribution of chromatin remodelers, DNA-binding proteins, and the differential affinity of nucleosomes for different DNA sequences. Chromatin remodelers are multiprotein complexes that use ATP hydrolysis to facilitate the sliding, eviction or histone exchange of nucleosomes.
A python package for nucleosome-positioning using as basis the highly structured pattern of DNA fragment lengths and positions around nucleosomes. NucleoATAC can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy in Schizosaccharomyces cerevisiae, Schizosaccharomyces pombe and human cells. NucleoATAC can be used to analyze sequence features underlying nucleosome positioning, to promote chromatin architecture across species, to identify transient changes in nucleosome occupancy and to asses positioning during a dynamic cellular response.
Evaluates cell-to-cell variation at a chromatin accessibility-level. PRISM supplies an R package based on a linear algebra-based method considering a set of sequence linked by a shared feature. This application exploits differences in accessibility of every genomic region of interest through individual cells. It can be used to estimate the effects of transcription factor binding on the chromatin accessibility or to highlight the grasp about epigenomic regulation in development and disease.