ArticleCurrent protocols in bioinformatics2019
R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi-C Datasets.
Article in Current protocols in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variants.PLoS pathogens · 2025Article
- HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data.Briefings in bioinformatics · 2022Article
- Methods for the Differential Analysis of Hi-C Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
4 authors.
Funding
Abstract
The three-dimensional (3D) interactions of chromatin regulate cell-type-specific gene expression, recombination, X-chromosome inactivation, and many other genomic processes. High-throughput chromatin conformation capture (Hi-C) technologies capture the structure of the chromatin on a global scale by measuring all-vs.-all interactions and can provide new insights into genomic regulation. The workflow presented here describes how to analyze and interpret a comparative Hi-C experiment. 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.
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Registered trials
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