RNAmodR

DOI: 10.18129/B9.bioc.RNAmodR    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see RNAmodR.

Detection of post-transcriptional modifications in high throughput sequencing data

Bioconductor version: 3.10

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 "3.6") and enter:

if (!requireNamespace("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	1.0.2
In Bioconductor since	BioC 3.10 (R-3.6) (< 6 months)
License	Artistic-2.0
Depends	R (>= 3.6), IRanges(>= 2.19.7), S4Vectors(>= 0.23.18), GenomicRanges, Modstrings
Imports	methods, stats, graphics, grDevices, grid, matrixStats, assertive, BiocGenerics, XVector, Biostrings, BiocParallel, GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, biovizBase, ggplot2, Gviz, reshape2, stringi, stringr, 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_1.0.2.tar.gz
Windows Binary	RNAmodR_1.0.2.zip
Mac OS X 10.11 (El Capitan)	RNAmodR_1.0.2.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