supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map.
supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map.
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DOI：
10.1016/j.bbrc.2013.11.103
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发表时间：
2014-01-03
影响因子：
3.1
通讯作者：
Gough, Julian
中科院分区：
文献类型：
--
作者：
Fang, Hai;Gough, Julian
supraHex是一个开源的R/Bioconductor软件包，用于表格组学数据分析。超六边形地图被设计用于自组织组学数据。supraHex图谱同时分析基因和样品。supraHex图可以被额外的数据覆盖，用于多层组学数据比较。supraHex可以揭示复制时间、CpG和表达之间的内在关系。生物学家越来越多地面临着快速理解全基因组生物数据的挑战，这些数据通常涉及大量的基因组坐标（例如基因），但样本数量要少得多。为了满足这种形状的数据的需求，我们提出了一个名为“supraHex”的开源软件包，用于训练，分析和可视化组学数据。该软件包设计了一个超六边形地图来自组织输入数据，提供了用于后分析地图的可扩展功能，更重要的是，允许叠加额外的数据进行多层组学数据比较。通过应用于小鼠胚胎发生的DNA复制定时数据，我们证明了supraHex能够同时进行基因聚类和样品相关，在分析的每一步提供直观的可视化。通过将CpG和表达数据叠加到训练的复制定时图上，我们还表明，supraHex能够直观地捕获后期复制、低CpG密度启动子和低表达水平之间的内在关系。作为Bioconductor项目的一部分，supraHex以简单的方式向广泛的社区提供访问，否则将是一个复杂的框架，用于超快速地理解任何表格组学数据，无论是科学还是艺术。这个软件包可以在Windows、Mac和Linux上运行，并且可以在http://supfam.org/supraHex上免费获得，还有许多关于真实的示例的教程。
supraHex is an open-source R/Bioconductor package for tabular omics data analysis. A supra-hexagonal map is designed to self-organise omics data. The supraHex map analyses both genes and samples at the same time. The supraHex map can be overlaid by additional data for multilayer omics data comparisons. supraHex can tell inherent relations between replication timing, CpG and expression. Biologists are increasingly confronted with the challenge of quickly understanding genome-wide biological data, which usually involve a large number of genomic coordinates (e.g. genes) but a much smaller number of samples. To meet the need for data of this shape, we present an open-source package called ‘supraHex’ for training, analysing and visualising omics data. This package devises a supra-hexagonal map to self-organise the input data, offers scalable functionalities for post-analysing the map, and more importantly, allows for overlaying additional data for multilayer omics data comparisons. Via applying to DNA replication timing data of mouse embryogenesis, we demonstrate that supraHex is capable of simultaneously carrying out gene clustering and sample correlation, providing intuitive visualisation at each step of the analysis. By overlaying CpG and expression data onto the trained replication-timing map, we also show that supraHex is able to intuitively capture an inherent relationship between late replication, low CpG density promoters and low expression levels. As part of the Bioconductor project, supraHex makes accessible to a wide community in a simple way, what would otherwise be a complex framework for the ultrafast understanding of any tabular omics data, both scientifically and artistically. This package can run on Windows, Mac and Linux, and is freely available together with many tutorials on featuring real examples at http://supfam.org/supraHex.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
DOI：
10.1073/pnas.96.6.2907
发表时间：
1999-03-16
影响因子：
11.1
作者：
Tamayo, P;Slonim, D;Golub, TR
通讯作者：
Golub, TR
影响因子：
64.8
作者：
Mikkelsen, Tarjei S.;Ku, Manching;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
影响因子：
5.8
作者：
de Hoon, MJL;Imoto, S;Miyano, S
通讯作者：
Miyano, S
影响因子：
46.9
作者：
Lockhart, DJ;Dong, HL;Brown, EL
通讯作者：
Brown, EL