RNAprobR

DOI: 10.18129/B9.bioc.RNAprobR    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RNAprobR.

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

Bioconductor version: 3.13

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 <kielpinski at bio.ku.dk>, Nikos Sidiropoulos <nikos.sidiro at gmail.com>, Jeppe Vinther <jvinther at bio.ku.dk>

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

Installation

To install this package, start R (version "4.1") 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

PDF		Reference Manual

Details

biocViews	Coverage, GenomeAnnotation, Normalization, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 3.1 (R-3.2) (6.5 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
Windows Binary
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/RNAprobR/
Package Downloads Report	Download Stats