R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi‐C Datasets

Nucleosome-free DNA regions differentially affect distant communication in chromatin

Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleosome spacing and the presence of nucleosome-free DNA regions can modulate chroma...

Simultaneous Sequential Detection of Multiple Interacting Faults

Single fault sequential change point problems have become important in modeling for various phenomena in large distributed systems, such as sensor networks. But such systems in many situations present multiple interacting faults. For example, individual sensors in a network may fail and detection is performed by comparing measurements between sensors, resulting in statistical dependency among f...

Robust Methods for Locating Multiple Dense Regions in Complex Datasets

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Tutorial - Multiple-QTL Mapping (MQM) Analysis for R/qtl

Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions

Analysis of bisulfite sequencing data usually requires two tasks: to call methylated cytosines (mCs) in a sample, and to detect differentially methylated regions (DMRs) between paired samples. Although numerous tools have been proposed for mC calling, methods for DMR detection have been largely limited. Here, we present Bisulfighter, a new software package for detecting mCs and DMRs from bisulf...