RNAmodR
This is the development version of RNAmodR; for the stable release version, see RNAmodR.
Detection of post-transcriptional modifications in high throughput sequencing data
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| 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 | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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 |
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_1.27.0.tar.gz |
| Windows Binary (x86_64) | RNAmodR_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | RNAmodR_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | RNAmodR_1.27.0.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 |