A1 Refereed original research article in a scientific journal

RepViz: A replicate-driven R tool for visualizing genomic regions




AuthorsFaux T., Rytkönen K., Laiho A., Elo L.

PublisherBioMed Central Ltd.

Publication year2019

JournalBMC Research Notes

Journal name in sourceBMC Research Notes

Article number441

Volume12

ISSN1756-0500

eISSN1756-0500

DOIhttps://doi.org/10.1186/s13104-019-4473-z

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/41752451


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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