scanMiRApp
This is the development version of scanMiRApp; for the stable release version, see scanMiRApp.
scanMiR shiny application
Bioconductor version: Development (3.21)
A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.
Author: Pierre-Luc Germain [cre, aut] (ORCID:
Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>
citation("scanMiRApp")):
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("scanMiRApp")
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("scanMiRApp")| IndexedFst | HTML | R Script |
| scanMiRApp | HTML | R Script |
| Reference Manual |
Details
| biocViews | GUI, SequenceMatching, ShinyApps, Software, miRNA |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.0), scanMiR |
| Imports | AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | scanMiRApp_1.13.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scanMiRApp |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scanMiRApp |
| Bioc Package Browser | https://code.bioconductor.org/browse/scanMiRApp/ |
| Package Short Url | https://bioconductor.org/packages/scanMiRApp/ |
| Package Downloads Report | Download Stats |