quantro
This is the development version of quantro; for the stable release version, see quantro.
A test for when to use quantile normalization
Bioconductor version: Development (3.24)
A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.
Author: Stephanie Hicks [aut, cre]
, Rafael Irizarry [aut]
Maintainer: Stephanie Hicks <shicks19 at jhu.edu>
citation("quantro")):
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("quantro")
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("quantro")| The quantro user's guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microarray, MultipleComparison, Normalization, Preprocessing, Sequencing, Software |
| Version | 1.47.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | GPL-3 |
| Depends | R (>= 4.0) |
| Imports | Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | yarn |
| Suggests Me | extraChIPs, qsmooth |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | quantro_1.47.0.tar.gz |
| Windows Binary (x86_64) | quantro_1.47.0.zip |
| macOS Binary (big-sur-x86_64) | quantro_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | quantro_1.47.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/quantro |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/quantro |
| Bioc Package Browser | https://code.bioconductor.org/browse/quantro/ |
| Package Short Url | https://bioconductor.org/packages/quantro/ |
| Package Downloads Report | Download Stats |