RNAprobR

This package is for version 3.10 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: 3.10

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 "3.6") 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

Details

biocViews Coverage, GenomeAnnotation, Normalization, Sequencing, Software
Version 1.18.0
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_1.18.0.tar.gz
Windows Binary RNAprobR_1.18.0.zip
Mac OS X 10.11 (El Capitan) RNAprobR_1.18.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive