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

We describe the process of obtaining Hi-C data from public repositories and give suggestions for pre-processing pipelines for users who intend to analyze their own raw data. We then describe the data normalization and comparative analysis process. We present three protocols describing the use of the multiHiCcompare, diffHic, and FIND R packages, respectively, to perform a comparative analysis of Hi-C experiments. Finally, visualization of the results and downstream interpretation of the differentially interacting regions are discussed. The bulk of this tutorial uses the R programming environment, and the processes described can be performed with most operating systems and a single computer. © 2019 by John Wiley & Sons, Inc. PMID: 31125519 [PubMed - as supplied by publisher]
Source: Current Protocols in Bioinformatics - Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research