DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.
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DOI：
10.1093/bioinformatics/btv735
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发表时间：
2016-04-15
期刊：
影响因子：
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通讯作者：
Rohs R
中科院分区：
文献类型：
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作者：
Chiu TP;Comoglio F;Zhou T;Yang L;Paro R;Rohs R
摘要：DNAshapeR从基因组测序数据中以超快、高通量的方式预测DNA形状特征。该软件包将核苷酸序列或基因组坐标作为输入，并生成各种图形表示，用于可视化和进一步分析。DNAshapeR进一步将DNA序列和形状特征编码为用户定义的k-mer和DNA形状特征的组合。所得到的特征矩阵可以很容易地用作各种机器学习软件包的输入，用于进一步的建模研究。可用性和实施：DNAshapeR软件包采用统计编程语言R实现，可通过Bioconductor项目https://www.bioconductor.org/packages/devel/bioc/html/DNAshapeR.html和GitHub开发人员网站http://tsupeichiu.github.io/DNAshapeR/。联系方式：rohs@usc.edu补充信息：补充数据可从生物信息学在线网站获得。
Summary: DNAshapeR predicts DNA shape features in an ultra-fast, high-throughput manner from genomic sequencing data. The package takes either nucleotide sequence or genomic coordinates as input and generates various graphical representations for visualization and further analysis. DNAshapeR further encodes DNA sequence and shape features as user-defined combinations of k-mer and DNA shape features. The resulting feature matrices can be readily used as input of various machine learning software packages for further modeling studies. Availability and implementation: The DNAshapeR software package was implemented in the statistical programming language R and is freely available through the Bioconductor project at https://www.bioconductor.org/packages/devel/bioc/html/DNAshapeR.html and at the GitHub developer site, http://tsupeichiu.github.io/DNAshapeR/. Contact: rohs@usc.edu Supplementary information: Supplementary data are available at Bioinformatics online.