RNAmodR

DOI: 10.18129/B9.bioc.RNAmodR    

This is the development version of RNAmodR; for the stable release version, see RNAmodR.

Detection of post-transcriptional modifications in high throughput sequencing data

Bioconductor version: Development (3.12)

RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.

Author: Felix G.M. Ernst [aut, cre] , Denis L.J. Lafontaine [ctb, fnd]

Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>

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

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RNAmodR")

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("RNAmodR")

 

HTML R Script RNAmodR
HTML R Script RNAmodR - creating new classes for a new detection strategy
PDF   Reference Manual
Text   NEWS

Details

biocViews Infrastructure, Sequencing, Software, Visualization, WorkflowStep
Version 1.3.4
In Bioconductor since BioC 3.10 (R-3.6) (1 year)
License Artistic-2.0
Depends R (>= 3.6), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), GenomicRanges, Modstrings
Imports methods, stats, grDevices, matrixStats, BiocGenerics, Biostrings(>= 2.57.2), BiocParallel, GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, ggplot2, grid, Gviz(>= 1.31.0), reshape2, graphics, ROCR
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data
SystemRequirements
Enhances
URL https://github.com/FelixErnst/RNAmodR
BugReports https://github.com/FelixErnst/RNAmodR/issues
Depends On Me RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package RNAmodR_1.3.4.tar.gz
Windows Binary RNAmodR_1.3.4.zip
macOS 10.13 (High Sierra) RNAmodR_1.3.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/RNAmodR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RNAmodR
Package Short Url https://bioconductor.org/packages/RNAmodR/
Package Downloads Report Download Stats

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