RNAmodR

DOI: 10.18129/B9.bioc.RNAmodR    

This is the development version of RNAmodR; to use it, please install the devel version of Bioconductor.

Detection of post-transcriptional modifications in high throughput sequencing data

Bioconductor version: Development (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>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.35
In Bioconductor since BioC 3.10 (R-3.6)
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_0.99.35.tar.gz
Windows Binary RNAmodR_0.99.35.zip
Mac OS X 10.11 (El Capitan) RNAmodR_0.99.35.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

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