RNAprobR

This package is for version 3.8 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

DOI: 10.18129/B9.bioc.RNAprobR

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>

Citation (from within R, enter citation("RNAprobR")):

Installation

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


if (!require("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")

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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, GenomeAnnotation, Normalization, Sequencing, Software

Version 1.14.0

In Bioconductor since BioC 3.1 (R-3.2) (9 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

Bioc Package Browser https://code.bioconductor.org/browse/RNAprobR/

Package Short Url https://bioconductor.org/packages/RNAprobR/

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Old Source Packages for BioC 3.8 Source Archive