OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data
Summary OmicCircos is an R software package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. Such variations can be displayed as scatterplot, line, or text-label...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2014-01-01
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| Series: | Cancer Informatics |
| Online Access: | https://doi.org/10.4137/CIN.S13495 |
| _version_ | 1818146606024753152 |
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| author | Ying Hu Chunhua Yan Chih-Hao Hsu Qing-Rong Chen Kelvin Niu George A. Komatsoulis Daoud Meerzaman |
| author_facet | Ying Hu Chunhua Yan Chih-Hao Hsu Qing-Rong Chen Kelvin Niu George A. Komatsoulis Daoud Meerzaman |
| author_sort | Ying Hu |
| collection | DOAJ |
| description | Summary OmicCircos is an R software package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. Such variations can be displayed as scatterplot, line, or text-label figures. Relationships among genomic features in different chromosome positions can be represented in the forms of polygons or curves. Utilizing the statistical and graphic functions in an R/Bioconductor environment, OmicCircos performs statistical analyses and displays results using cluster, boxplot, histogram, and heatmap formats. In addition, OmicCircos offers a number of unique capabilities, including independent track drawing for easy modification and integration, zoom functions, link-polygons, and position-independent heatmaps supporting detailed visualization. Availability and Implementation OmicCircos is available through Bioconductor at http://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html . An extensive vignette in the package describes installation, data formatting, and workflow procedures. The software is open source under the Artistic—2.0 license. |
| first_indexed | 2024-12-11T12:22:01Z |
| format | Article |
| id | doaj.art-0fd3a7e6013a448a8496cba86ed11c33 |
| institution | Directory Open Access Journal |
| issn | 1176-9351 |
| language | English |
| last_indexed | 2024-12-11T12:22:01Z |
| publishDate | 2014-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Cancer Informatics |
| spelling | doaj.art-0fd3a7e6013a448a8496cba86ed11c332022-12-22T01:07:30ZengSAGE PublishingCancer Informatics1176-93512014-01-011310.4137/CIN.S13495OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics DataYing Hu0Chunhua Yan1Chih-Hao Hsu2Qing-Rong Chen3Kelvin Niu4George A. Komatsoulis5Daoud Meerzaman6Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.Summary OmicCircos is an R software package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. Such variations can be displayed as scatterplot, line, or text-label figures. Relationships among genomic features in different chromosome positions can be represented in the forms of polygons or curves. Utilizing the statistical and graphic functions in an R/Bioconductor environment, OmicCircos performs statistical analyses and displays results using cluster, boxplot, histogram, and heatmap formats. In addition, OmicCircos offers a number of unique capabilities, including independent track drawing for easy modification and integration, zoom functions, link-polygons, and position-independent heatmaps supporting detailed visualization. Availability and Implementation OmicCircos is available through Bioconductor at http://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html . An extensive vignette in the package describes installation, data formatting, and workflow procedures. The software is open source under the Artistic—2.0 license.https://doi.org/10.4137/CIN.S13495 |
| spellingShingle | Ying Hu Chunhua Yan Chih-Hao Hsu Qing-Rong Chen Kelvin Niu George A. Komatsoulis Daoud Meerzaman OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data Cancer Informatics |
| title | OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data |
| title_full | OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data |
| title_fullStr | OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data |
| title_full_unstemmed | OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data |
| title_short | OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data |
| title_sort | omiccircos a simple to use r package for the circular visualization of multidimensional omics data |
| url | https://doi.org/10.4137/CIN.S13495 |
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