Unknown

Dataset Information

0

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


ABSTRACT: 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.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.eduSupplementary data are available at Bioinformatics online.

SUBMITTER: Chiu TP 

PROVIDER: S-EPMC4824130 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

altmetric image

Publications

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

Chiu Tsu-Pei TP   Comoglio Federico F   Zhou Tianyin T   Yang Lin L   Paro Renato R   Rohs Remo R  

Bioinformatics (Oxford, England) 20151214 8


<h4>Unlabelled</h4>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  ...[more]

Similar Datasets

| S-EPMC8201924 | biostudies-literature
| S-EPMC5761903 | biostudies-literature
| S-EPMC6584971 | biostudies-literature
| S-EPMC4016708 | biostudies-literature
| S-EPMC11348166 | biostudies-literature
| S-EPMC6041802 | biostudies-other
| S-EPMC2777013 | biostudies-literature
| S-EPMC10582516 | biostudies-literature
| S-EPMC3892686 | biostudies-literature
| S-EPMC7904076 | biostudies-literature