miRNAtap
This is the development version of miRNAtap; for the stable release version, see miRNAtap.
miRNAtap: microRNA Targets - Aggregated Predictions
Bioconductor version: Development (3.24)
The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).
Author: Maciej Pajak, T. Ian Simpson
Maintainer: T. Ian Simpson <ian.simpson at ed.ac.uk>
citation("miRNAtap")):
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("miRNAtap")
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("miRNAtap")| miRNAtap | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Microarray, Sequencing, Software, miRNA |
| Version | 1.47.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | GPL-2 |
| Depends | R (>= 3.3.0), AnnotationDbi |
| Imports | DBI, RSQLite, stringr, sqldf, plyr, methods |
| System Requirements | |
| URL |
See More
| Suggests | topGO, org.Hs.eg.db, miRNAtap.db, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | miRNAtap.db |
| Imports Me | miRNAtap.db |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | miRNAtap_1.47.0.tar.gz |
| Windows Binary (x86_64) | miRNAtap_1.47.0.zip |
| macOS Binary (big-sur-x86_64) | miRNAtap_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | miRNAtap_1.47.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/miRNAtap |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/miRNAtap |
| Bioc Package Browser | https://code.bioconductor.org/browse/miRNAtap/ |
| Package Short Url | https://bioconductor.org/packages/miRNAtap/ |
| Package Downloads Report | Download Stats |