RNAprobR

DOI: 10.18129/B9.bioc.RNAprobR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RNAprobR.

An R package for analysis of massive parallel sequencing based RNA structure probing data

Bioconductor version: 3.8

This package facilitates analysis of Next Generation Sequencing data for which positional information with a single nucleotide resolution is a key. It allows for applying different types of relevant normalizations, data visualization and export in a table or UCSC compatible bedgraph file.

Author: Lukasz Jan Kielpinski [aut], Nikos Sidiropoulos [cre, aut], Jeppe Vinther [aut]

Maintainer: Nikos Sidiropoulos <nikos.sidiro at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("RNAprobR")

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("RNAprobR")

 

PDF	R Script	RNAprobR: An R package for analysis of the massive parallel sequencing based methods of RNA structure probing
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, GenomeAnnotation, Normalization, Sequencing, Software
Version	1.14.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 years)
License	GPL (>=2)
Depends	R (>= 3.1.1), GenomicFeatures(>= 1.16.3), plyr (>= 1.8.1), BiocGenerics(>= 0.10.0)
Imports	Biostrings(>= 2.32.1), GenomicRanges(>= 1.16.4), IRanges(>= 2.10.5), Rsamtools(>= 1.16.1), rtracklayer(>= 1.24.2), GenomicAlignments(>= 1.5.12), S4Vectors(>= 0.14.7), graphics, stats, utils
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RNAprobR_1.14.0.tar.gz
Windows Binary	RNAprobR_1.14.0.zip
Mac OS X 10.11 (El Capitan)	RNAprobR_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RNAprobR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RNAprobR
Package Short Url	http://bioconductor.org/packages/RNAprobR/
Package Downloads Report	Download Stats