RNAmodR
Detection of post-transcriptional modifications in high throughput sequencing data
Bioconductor version: Release (3.19)
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 "4.4") 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 | 1.18.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (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, txdbmaker, 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_1.18.0.tar.gz |
Windows Binary | RNAmodR_1.18.0.zip (64-bit only) |
macOS Binary (x86_64) | RNAmodR_1.18.0.tgz |
macOS Binary (arm64) | RNAmodR_1.18.0.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 |