RNAmodR

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

Detection of post-transcriptional modifications in high throughput sequencing data

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DOI: 10.18129/B9.bioc.RNAmodR

Bioconductor version: Release (3.22)

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 iD 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")):

Installation

To install this package, start R (version "4.5") 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 1.24.0

In Bioconductor since BioC 3.10 (R-3.6) (6 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

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Package Archives

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

Source Package RNAmodR_1.24.0.tar.gz

Windows Binary (x86_64) RNAmodR_1.24.0.zip

macOS Binary (x86_64) RNAmodR_1.24.0.tgz

macOS Binary (arm64) RNAmodR_1.24.0.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/

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