MOTIVATION: Deciphering nucleosome-nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. RESULTS: We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools. AVAILABILITYAND IMPLEMENTATION: https://github.com/Karimi-Lab/inucs/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The AGM paradigm of belief change studies the dynamics of belief states in light of new information. Finding, or even approximating, those beliefs that are dependent on or relevant to a change is valuable because, for example, it can narrow the set of beliefs considered during belief change operations. A strong intuition in this area is captured by Gärdenfors’s preservation criterion (GPC), which suggests that formulas independent of a belief change should remain intact. GPC thus allows one to build dependence relations that are linked with belief change. Such dependence relations can in turn be used as a theoretical benchmark against which to evaluate other approximate dependence or relevance relations. Fariñas and Herzig axiomatize a dependence relation with respect to a belief set, and, based on GPC, they characterize the correspondence between AGM contraction functions and dependence relations. In this paper, we introduce base dependence as a relation between formulas with respect to a belief base, and prove a more general characterization that shows the correspondence between kernel contraction and base dependence. At this level of generalization, different types of base dependence emerge, which we show to be a result of possible redundancy in the belief base. We further show that one of these relations that emerge, strong base dependence, is parallel to saturated kernel contraction. We then prove that our latter characterization is a reversible generalization of Fariñas and Herzig’s characterization. That is, in the special case when the underlying belief base is deductively closed (i.e., it is a belief set), strong base dependence reduces to dependence, and so do their respective characterizations. Finally, an intriguing feature of Fariñas and Herzig’s formalism is that it meets other criteria for dependence, namely, Keynes’s conjunction criterion for dependence (CCD) and Gärdenfors’s conjunction criterion for independence (CCI). We prove that our base dependence formalism also meets these criteria. Even more interestingly, we offer a more specific criterion that implies both CCD and CCI, and show our base dependence formalism also meets this new criterion.