RNAmodR

This is the released version of RNAmodR; for the devel version, see RNAmodR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10

Detection of post-transcriptional modifications in high throughput sequencing data

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-5064-0928 , Denis L.J. Lafontaine [ctb, fnd]

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

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

Felix G.M. Ernst. RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data. doi:10.18129/B9.bioc.RNAmodR, R package version 1.26.0, https://bioconductor.org/packages/RNAmodR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, Sequencing, Software, Visualization, WorkflowStep
Version	1.26.0
In Bioconductor since	BioC 3.10 (R-3.6) (7 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, txdbmaker, GenomicFeatures, GenomicAlignments, Seqinfo, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, ggplot2, Gviz (>= 1.31.0), reshape2, graphics, ROCR
System Requirements
URL	https://github.com/FelixErnst/RNAmodR
Bug Reports	https://github.com/FelixErnst/RNAmodR/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data
Linking To
Enhances
Depends On Me	RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	RNAmodR_1.26.0.tar.gz
Windows Binary (x86_64)	RNAmodR_1.26.0.zip
macOS Binary (big-sur-x86_64)	RNAmodR_1.26.0.tgz
macOS Binary (sonoma-arm64)	RNAmodR_1.26.0.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