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RNAmodR

Detection of post-transcriptional modifications in high throughput sequencing data


Bioconductor version: Release (3.18)

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

Details

biocViews Infrastructure, Sequencing, Software, Visualization, WorkflowStep
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
System Requirements
URL https://github.com/FelixErnst/RNAmodR
Bug Reports https://github.com/FelixErnst/RNAmodR/issues
See More
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

Package Archives

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

Source Package RNAmodR_1.16.0.tar.gz
Windows Binary RNAmodR_1.16.0.zip
macOS Binary (x86_64) RNAmodR_1.16.0.tgz
macOS Binary (arm64) RNAmodR_1.16.0.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