RNAmodR

DOI: 10.18129/B9.bioc.RNAmodR  

Detection of post-transcriptional modifications in high throughput sequencing data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
License	Artistic-2.0
Depends	R (>= 4.0), 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, 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_1.12.0.tar.gz
Windows Binary	RNAmodR_1.12.0.zip
macOS Binary (x86_64)	RNAmodR_1.12.0.tgz
macOS Binary (arm64)	RNAmodR_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RNAmodR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RNAmodR
Bioc Package Browser	https://code.bioconductor.org/browse/RNAmodR/
Package Short Url	https://bioconductor.org/packages/RNAmodR/
Package Downloads Report	Download Stats