DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

被引：109

作者：

Chiu, Tsu-Pei ^{[1
,2
,3
,4
]}

Comoglio, Federico ^{[5
]}

Zhou, Tianyin ^{[1
,2
,3
,4
]}

Yang, Lin ^{[1
,2
,3
,4
]}

Paro, Renato ^{[5
,6
]}

Rohs, Remo ^{[1
,2
,3
,4
]}

机构：

[1] Univ So Calif, Dept Biol Sci, Mol & Computat Biol Program, Los Angeles, CA 90089 USA

[2] Univ So Calif, Dept Chem, Los Angeles, CA 90089 USA

[3] Univ So Calif, Dept Phys, Los Angeles, CA 90089 USA

[4] Univ So Calif, Dept Comp Sci, Los Angeles, CA 90089 USA

[5] ETH, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland

[6] Univ Basel, Fac Sci, Klingelbergstr 50, CH-4056 Basel, Switzerland

来源：

BIOINFORMATICS | 2016年 / 32卷 / 08期

基金：

美国国家科学基金会;

关键词：

DATABASE; SITES;

D O I：

10.1093/bioinformatics/btv735

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A 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.

引用

页码：1211 / 1213

页数：3

共 8 条

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