ncRNAtools
This is the released version of ncRNAtools; for the devel version, see ncRNAtools.
An R toolkit for non-coding RNA
Bioconductor version: Release (3.23)
ncRNAtools provides a set of basic tools for handling and analyzing non-coding RNAs. These include tools to access the RNAcentral database and to predict and visualize the secondary structure of non-coding RNAs. The package also provides tools to read, write and interconvert the file formats most commonly used for representing such secondary structures.
Author: Lara Selles Vidal [cre, aut]
, Rafael Ayala [aut]
, Guy-Bart Stan [aut]
, Rodrigo Ledesma-Amaro [aut]
Maintainer: Lara Selles Vidal <lara.selles at oist.jp>
citation("ncRNAtools")):
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("ncRNAtools")
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("ncRNAtools")| rfaRm | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, FunctionalGenomics, Software, StructuralPrediction, ThirdPartyClient, Visualization |
| Version | 1.22.2 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | |
| Imports | httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/LaraSellesVidal/ncRNAtools/issues |
See More
| Suggests | knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics |
| Linking To | |
| 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 | ncRNAtools_1.22.2.tar.gz |
| Windows Binary (x86_64) | ncRNAtools_1.22.2.zip |
| macOS Binary (big-sur-x86_64) | ncRNAtools_1.22.2.tgz |
| macOS Binary (sonoma-arm64) | ncRNAtools_1.22.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ncRNAtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ncRNAtools |
| Bioc Package Browser | https://code.bioconductor.org/browse/ncRNAtools/ |
| Package Short Url | https://bioconductor.org/packages/ncRNAtools/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |