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.

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

Bioconductor version: Release (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>

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

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 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
LinkingTo
Suggests BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: