RNAmodR
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RNAmodR.
Detection of post-transcriptional modifications in high throughput sequencing data
Bioconductor version: 3.12
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("RNAmodR")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Sequencing, Software, Visualization, WorkflowStep |
| Version | 1.4.2 |
| 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_1.4.2.tar.gz |
| Windows Binary | RNAmodR_1.4.2.zip |
| macOS 10.13 (High Sierra) | RNAmodR_1.4.2.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 3.12 | Source Archive |