ExiMiR
This is the released version of ExiMiR; for the devel version, see ExiMiR.
R functions for the normalization of Exiqon miRNA array data
Bioconductor version: Release (3.23)
This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.
Author: Sylvain Gubian <DL.RSupport at pmi.com>, Alain Sewer <DL.RSupport at pmi.com>, PMP SA
Maintainer: Sylvain Gubian <DL.RSupport at pmi.com>
citation("ExiMiR")):
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")
BiocManager::install("ExiMiR")
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("ExiMiR")| Description of ExiMiR | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Microarray, OneChannel, Preprocessing, Software, Transcription, TwoChannel |
| Version | 2.54.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (15.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.10), Biobase(>= 2.5.5), affy(>= 1.26.1), limma |
| Imports | affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) |
| System Requirements | |
| URL |
See More
| Suggests | mirna10cdf |
| 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 | ExiMiR_2.54.0.tar.gz |
| Windows Binary (x86_64) | ExiMiR_2.54.0.zip |
| macOS Binary (big-sur-x86_64) | ExiMiR_2.54.0.tgz |
| macOS Binary (sonoma-arm64) | ExiMiR_2.54.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ExiMiR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ExiMiR |
| Bioc Package Browser | https://code.bioconductor.org/browse/ExiMiR/ |
| Package Short Url | https://bioconductor.org/packages/ExiMiR/ |
| Package Downloads Report | Download Stats |