A1 Journal article – refereed
RepViz: A replicate-driven R tool for visualizing genomic regions




List of Authors: Faux T., Rytkönen K., Laiho A., Elo L.
Publisher: BioMed Central Ltd.
Publication year: 2019
Journal: BMC Research Notes
Journal name in source: BMC Research Notes
Volume number: 12
ISSN: 1756-0500
eISSN: 1756-0500

Abstract

Objective: Visualization of sequencing data is an integral part of genomic data analysis. Although there are several
tools to visualize sequencing data on genomic regions, they do not ofer user-friendly ways to view simultaneously
diferent groups of replicates. To address this need, we developed a tool that allows efcient viewing of both intraand intergroup variation of sequencing counts on a genomic region, as well as their comparison to the output of user
selected analysis methods, such as peak calling. 

Results: We present an R package RepViz for replicate-driven visualization of genomic regions. With ChIP-seq and
ATAC-seq data we demonstrate its potential to aid visual inspection involved in the evaluation of normalization, outlier behavior, detected features from diferential peak calling analysis, and combined analysis of multiple data types.
RepViz is readily available on Bioconductor (https://www.bioconductor.org/packages/devel/bioc/html/RepViz.html)
and on Github (https://github.com/elolab/RepViz).


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Last updated on 2019-03-09 at 13:20