Dataset Information

RepViz: a replicate-driven R tool for visualizing genomic regions.

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 offer user-friendly ways to view simultaneously different groups of replicates. To address this need, we developed a tool that allows efficient viewing of both intra- and 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 differential 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 ).

SUBMITTER: Faux T

PROVIDER: S-EPMC6642542 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Publications

RepViz: a replicate-driven R tool for visualizing genomic regions.

Faux Thomas T Rytkönen Kalle T KT Laiho Asta A Elo Laura L LL

BMC research notes 20190719 1

<h4>Objective</h4>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 offer user-friendly ways to view simultaneously different groups of replicates. To address this need, we developed a tool that allows efficient viewing of both intra- and intergroup variation of sequencing counts on a genomic region, as well as their comparison to the output of user selected analysis methods ...[more]

PMID: 31324268

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Dataset Information

RepViz: a replicate-driven R tool for visualizing genomic regions.

Objective

Results

Publications

RepViz: a replicate-driven R tool for visualizing genomic regions.

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