RNAmodR
Detection of post-transcriptional modifications in high throughput sequencing data
Bioconductor version: 3.23 · Package version: 1.26.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RNAmodR")Details
| Maintainer | Felix G.M. Ernst <felix.gm.ernst@outlook.com> |
| Author | Felix G.M. Ernst [aut, cre] (ORCID: <https://orcid.org/0000-0001-5064-0928>), Denis L.J. Lafontaine [ctb, fnd] |
| License | Artistic-2.0 |
| URL | https://github.com/FelixErnst/RNAmodR |
| Bug Reports | https://github.com/FelixErnst/RNAmodR/issues |
| Downloads rank | 337 |
| Source branch | RELEASE_3_23 |
| biocViews | Infrastructure, Sequencing, Software, Visualization, WorkflowStep |
Documentation
- RNAmodR: analyzing high throughput sequencing data for post-transcriptional RNA modification footprints
- RNAmodR: creating classes for additional modification detection from high throughput sequencing.
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Dependencies
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
Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data
Reverse dependencies
Depends On Me (3): RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq