RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms.
RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms.
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DOI：
10.7717/peerj-cs.251
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Chen J
中科院分区：
文献类型：
--
作者：
Hao Z;Lv D;Ge Y;Shi J;Weijers D;Yu G;Chen J
由于DNA测序技术的快速发展，越来越多物种的全基因组正以越来越快的速度变得可用。在全基因组分析中，个体基因图提供了一种非常流行、直观和有效的方法来绘制和可视化全基因组信息，如GC含量、基因和重复序列密度、DNA甲基化分布、基因组同线性等。然而，大多数可用的软件程序和Web服务器仅适用于少数模式物种，如人、小鼠和苍蝇，或者应用场景有限。随着越来越多的非模式物种被测序，染色体水平的组装是可用的，工具，可以生成idiogram为广泛的物种，并能够可视化更多的数据类型，以帮助更好地了解基本的基因组特征。R包RIdeogram允许用户构建任何感兴趣物种的高质量idigram。它可以将连续和离散的全基因组数据映射到idiogram上，并分别在热图和跟踪标签中将其可视化。全基因组数据映射和比较的可视化使用户能够快速建立染色体分布模式的清晰印象，从而使Rideogram成为任何从事组学研究的研究人员的有用工具。
Owing to the rapid advances in DNA sequencing technologies, whole genome from more and more species are becoming available at increasing pace. For whole-genome analysis, idiograms provide a very popular, intuitive and effective way to map and visualize the genome-wide information, such as GC content, gene and repeat density, DNA methylation distribution, genomic synteny, etc. However, most available software programs and web servers are available only for a few model species, such as human, mouse and fly, or have limited application scenarios. As more and more non-model species are sequenced with chromosome-level assembly being available, tools that can generate idiograms for a broad range of species and be capable of visualizing more data types are needed to help better understanding fundamental genome characteristics. The R package RIdeogram allows users to build high-quality idiograms of any species of interest. It can map continuous and discrete genome-wide data on the idiograms and visualize them in a heat map and track labels, respectively. The visualization of genome-wide data mapping and comparison allow users to quickly establish a clear impression of the chromosomal distribution pattern, thus making RIdeogram a useful tool for any researchers working with omics.