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EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations
BACKGROUND: High-throughput sequencing data are dramatically increasing in volume. Thus, there is urgent need for efficient tools to perform fast and integrative analysis of multiple data types. Enriched heatmap is a specific form of heatmap that visualizes how genomic signals are enriched over spec...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885322/ https://www.ncbi.nlm.nih.gov/pubmed/29618320 http://dx.doi.org/10.1186/s12864-018-4625-x |
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author | Gu, Zuguang Eils, Roland Schlesner, Matthias Ishaque, Naveed |
author_facet | Gu, Zuguang Eils, Roland Schlesner, Matthias Ishaque, Naveed |
author_sort | Gu, Zuguang |
collection | PubMed |
description | BACKGROUND: High-throughput sequencing data are dramatically increasing in volume. Thus, there is urgent need for efficient tools to perform fast and integrative analysis of multiple data types. Enriched heatmap is a specific form of heatmap that visualizes how genomic signals are enriched over specific target regions. It is commonly used and efficient at revealing enrichment patterns especially for high dimensional genomic and epigenomic datasets. RESULTS: We present a new R package named EnrichedHeatmap that efficiently visualizes genomic signal enrichment. It provides advanced solutions for normalizing genomic signals within target regions as well as offering highly customizable visualizations. The major advantage of EnrichedHeatmap is the ability to conveniently generate parallel heatmaps as well as complex annotations, which makes it easy to integrate and visualize comprehensive overviews of the patterns and associations within and between complex datasets. CONCLUSIONS: EnrichedHeatmap facilitates comprehensive understanding of high dimensional genomic and epigenomic data. The power of EnrichedHeatmap is demonstrated by visualization of the complex associations between DNA methylation, gene expression and various histone modifications. |
format | Online Article Text |
id | pubmed-5885322 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-58853222018-04-09 EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations Gu, Zuguang Eils, Roland Schlesner, Matthias Ishaque, Naveed BMC Genomics Software BACKGROUND: High-throughput sequencing data are dramatically increasing in volume. Thus, there is urgent need for efficient tools to perform fast and integrative analysis of multiple data types. Enriched heatmap is a specific form of heatmap that visualizes how genomic signals are enriched over specific target regions. It is commonly used and efficient at revealing enrichment patterns especially for high dimensional genomic and epigenomic datasets. RESULTS: We present a new R package named EnrichedHeatmap that efficiently visualizes genomic signal enrichment. It provides advanced solutions for normalizing genomic signals within target regions as well as offering highly customizable visualizations. The major advantage of EnrichedHeatmap is the ability to conveniently generate parallel heatmaps as well as complex annotations, which makes it easy to integrate and visualize comprehensive overviews of the patterns and associations within and between complex datasets. CONCLUSIONS: EnrichedHeatmap facilitates comprehensive understanding of high dimensional genomic and epigenomic data. The power of EnrichedHeatmap is demonstrated by visualization of the complex associations between DNA methylation, gene expression and various histone modifications. BioMed Central 2018-04-04 /pmc/articles/PMC5885322/ /pubmed/29618320 http://dx.doi.org/10.1186/s12864-018-4625-x Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Gu, Zuguang Eils, Roland Schlesner, Matthias Ishaque, Naveed EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations |
title | EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations |
title_full | EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations |
title_fullStr | EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations |
title_full_unstemmed | EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations |
title_short | EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations |
title_sort | enrichedheatmap: an r/bioconductor package for comprehensive visualization of genomic signal associations |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885322/ https://www.ncbi.nlm.nih.gov/pubmed/29618320 http://dx.doi.org/10.1186/s12864-018-4625-x |
work_keys_str_mv | AT guzuguang enrichedheatmapanrbioconductorpackageforcomprehensivevisualizationofgenomicsignalassociations AT eilsroland enrichedheatmapanrbioconductorpackageforcomprehensivevisualizationofgenomicsignalassociations AT schlesnermatthias enrichedheatmapanrbioconductorpackageforcomprehensivevisualizationofgenomicsignalassociations AT ishaquenaveed enrichedheatmapanrbioconductorpackageforcomprehensivevisualizationofgenomicsignalassociations |