chromPlot: visualization of genomic data in chromosomal context
chromPlot: visualization of genomic data in chromosomal context
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DOI：
10.1093/bioinformatics/btw137
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发表时间：
2016-08-01
期刊：
影响因子：
5.8
通讯作者：
Verdugo, Ricardo A.
中科院分区：
文献类型：
--
作者：
Orostica, Karen Y.;Verdugo, Ricardo A.
在染色体背景下可视化基因组数据可以帮助发现数据处理中的错误，并可能提出新的假设进行测试。在这里，我们报告了一种新的工具，用于显示沿染色体的大而多样的基因组数据。该软件是用R语言实现的，因此可视化可以很容易地与它的许多处理基因组数据的软件包集成在一起。它支持同时可视化多个数据轨道。大的基因组区域，如qtl或合成束，可以沿着基因数量、遗传变异或任何其他类型的基因组元件的直方图显示。轨迹还可以包含连续变量或分类变量的值，用户可以选择点、连接线、彩色段或直方图来表示数据。chromPlot从data中的表中获取数据。GRanges格式的帧。绘制小鼠和人类染色体所需的信息包含在包中。对于其他生物体，chromPlot可以从UCSC基因组浏览器读取Gap和cytobanddideo表。我们在这里展示了常见的用例，并包含了一个完整的教程作为包的小插图。可用性和实现：chromPlot在GLP2许可下发布在http://www.bioconductor.org。
Visualizing genomic data in chromosomal context can help detecting errors in data processing and may suggest new hypotheses to be tested. Here, we report a new tool for displaying large and diverse genomic data along chromosomes. The software is implemented in R so that visualization can be easily integrated with its numerous packages for processing genomic data. It supports simultaneous visualization of multiple tracks of data. Large genomic regions such as QTLs or synteny tracts may be shown along histograms of number of genes, genetic variants, or any other type of genomic element. Tracks can also contain values for continuous or categorical variables and the user can choose among points, connected lines, colored segments, or histograms for representing data. chromPlot takes data from tables in data. frame in GRanges formats. The information necessary to draw chromosomes for mouse and human is included with the package. For other organisms, chromPlot can read Gap and cytoBandIdeo tables from the UCSC Genome Browser. We present common use cases here, and a full tutorial is included as the package's vignette.Availability and Implementation: chromPlot is distributed under a GLP2 licence at http://www.bioconductor.org.