scanMiR
This is the development version of scanMiR; for the stable release version, see scanMiR.
scanMiR
Bioconductor version: Development (3.21)
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).
Author: Pierre-Luc Germain [cre, aut] (ORCID:
Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>
citation("scanMiR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scanMiR")
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("scanMiR")| 1_scanning | HTML | R Script |
| 2_Kdmodels | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, SequenceMatching, Software, miRNA |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.0) |
| Imports | Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | scanMiRApp |
| Imports Me | scanMiRData |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scanMiR_1.13.0.tar.gz |
| Windows Binary (x86_64) | scanMiR_1.13.0.zip (64-bit only) |
| macOS Binary (x86_64) | scanMiR_1.13.0.tgz |
| macOS Binary (arm64) | scanMiR_1.13.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scanMiR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scanMiR |
| Bioc Package Browser | https://code.bioconductor.org/browse/scanMiR/ |
| Package Short Url | https://bioconductor.org/packages/scanMiR/ |
| Package Downloads Report | Download Stats |