DNAshapeR
This is the released version of DNAshapeR; for the devel version, see DNAshapeR.
High-throughput prediction of DNA shape features
Bioconductor version: Release (3.23)
DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.
Author: Tsu-Pei Chiu and Federico Comoglio
Maintainer: Tsu-Pei Chiu <tsupeich at usc.edu>
citation("DNAshapeR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
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 JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DNAshapeR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DNAshapeR")| DNAshapeR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNA3DStructure, Software, StructuralPrediction |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.4), GenomicRanges |
| Imports | Rcpp (>= 0.12.1), Biostrings, fields |
| System Requirements | |
| URL |
See More
| Suggests | AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DNAshapeR_1.40.0.tar.gz |
| Windows Binary (x86_64) | DNAshapeR_1.40.0.zip |
| macOS Binary (big-sur-x86_64) | DNAshapeR_1.40.0.tgz |
| macOS Binary (sonoma-arm64) | DNAshapeR_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DNAshapeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DNAshapeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/DNAshapeR/ |
| Package Short Url | https://bioconductor.org/packages/DNAshapeR/ |
| Package Downloads Report | Download Stats |