marray
This is the released version of marray; for the devel version, see marray.
Exploratory analysis for two-color spotted microarray data
Bioconductor version: Release (3.23)
Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.
Author: Yee Hwa (Jean) Yang <jeany at maths.usyd.edu.au> with contributions from Agnes Paquet and Sandrine Dudoit.
Maintainer: Yee Hwa (Jean) Yang <jean at biostat.ucsf.edu>
citation("marray")):
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("marray")
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("marray")| marray Normalization | R Script | |
| marray Overview | R Script | |
| marrayClasses Overview | R Script | |
| marrayClasses Tutorial (short) | R Script | |
| marrayInput Introduction | R Script | |
| marrayPlots Overview | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Microarray, Preprocessing, Software, TwoChannel |
| Version | 1.90.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | LGPL |
| Depends | R (>= 2.10.0), limma, methods |
| Imports | |
| System Requirements | |
| URL | http://www.maths.usyd.edu.au/u/jeany/ |
See More
| Suggests | tkWidgets |
| Linking To | |
| Enhances | |
| Depends On Me | CGHbase, convert, dyebias, nnNorm, OLIN, RBM, stepNorm, TurboNorm, beta7, dyebiasexamples |
| Imports Me | arrayQuality, ChAMP, methylPipe, MSstats, MSstatsShiny, nnNorm, OLIN, OLINgui, piano, stepNorm, timecourse |
| Suggests Me | DEGraph, Mfuzz, hexbin |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | marray_1.90.0.tar.gz |
| Windows Binary (x86_64) | marray_1.90.0.zip |
| macOS Binary (big-sur-x86_64) | marray_1.90.0.tgz |
| macOS Binary (sonoma-arm64) | marray_1.90.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/marray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/marray |
| Bioc Package Browser | https://code.bioconductor.org/browse/marray/ |
| Package Short Url | https://bioconductor.org/packages/marray/ |
| Package Downloads Report | Download Stats |