RNAmodR

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see RNAmodR.

Detection of post-transcriptional modifications in high throughput sequencing data

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Infrastructure, Sequencing, Software, Visualization, WorkflowStep

Version 1.8.0

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

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_1.8.0.tar.gz

Windows Binary RNAmodR_1.8.0.zip

macOS 10.13 (High Sierra) RNAmodR_1.8.0.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

Old Source Packages for BioC 3.14 Source Archive