scanMiR
scanMiR
Bioconductor version: 3.23 · Package version: 1.18.0
A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scanMiR")Details
| Maintainer | Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch> |
| Author | Pierre-Luc Germain [cre, aut] (ORCID: <https://orcid.org/0000-0003-3418-4218>), Michael Soutschek [aut], Fridolin Gross [aut] |
| License | GPL-3 |
| Downloads rank | 280 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, SequenceMatching, Software, miRNA |
Documentation
- Scanning sequences for miRNA binding sites and exploring matches with scanMiR
- miRNA affinity models and the KdModel class
Download
Dependencies
Depends: R (>= 4.0)
Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, Seqinfo, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)