aroma.light
This is the released version of aroma.light; for the devel version, see aroma.light.
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Bioconductor version: Release (3.20)
Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.
Author: Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [ctb], Aaron Lun [ctb]
Maintainer: Henrik Bengtsson <henrikb at braju.com>
citation("aroma.light")):
Bengtsson H, Neuvial P, Speed TP (2010). “TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays.” BMC Bioinformatics, 11(245). doi:10.1186/1471-2105-11-245, https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-245.
Bengtsson H, Ray A, Spellman P, Speed TP (2009). “A single-sample method for normalizing and combining full-resolutioncopy numbers from multiple platforms, labs and analysis methods.” Bioinformatics, 25(7). doi:10.1093/bioinformatics/btp074, https://bioinformatics.oxfordjournals.org/cgi/content/full/25/7/861.
Bengtsson H, Simpson K, Bullard J, Hansen K (2008). “aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory.” Technical Report 745, Department of Statistics, University of California, Berkeley.
Bengtsson H, Irizarry R, Carvalho B, Speed T (2008). “Estimation and assessment of raw copy numbers at the single locus level.” Bioinformatics, 24(6). https://bioinformatics.oxfordjournals.org/cgi/content/full/24/6/759.
Bengtsson H, H"ossjer O (2006). “Methodological study of affine transformations of gene expressiondata with proposed robust non-parametric multi-dimensional normalization method.” BMC Bioinformatics, 7(100). doi:10.1186/1471-2105-7-100, https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-100.
Bengtsson H, J"onsson G, Vallon-Christersson J (2004). “Calibration and assessment of channel-specific biases in microarray data with extended dynamical range.” BMC Bioinformatics, 5(177). doi:10.1186/1471-2105-5-177, https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-177.
Bengtsson H (2004). “aroma - An R Object-oriented Microarray Analysis environment.” Preprint in Mathematical Sciences 18, Mathematical Statistics, Centre for Mathematical Sciences, Lund University, Sweden. https://lup.lub.lu.se/search/publication/929031.
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("aroma.light")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Infrastructure, Microarray, MultiChannel, OneChannel, Preprocessing, Software, TwoChannel, Visualization |
| Version | 3.36.0 |
| In Bioconductor since | BioC 1.9 (R-2.4) (18.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15.2) |
| Imports | stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) |
| System Requirements | |
| URL | https://github.com/HenrikBengtsson/aroma.light https://www.aroma-project.org |
| Bug Reports | https://github.com/HenrikBengtsson/aroma.light/issues |
See More
| Suggests | princurve (>= 2.1.4) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | EDASeq, scone, PSCBS |
| Suggests Me | TIN, aroma.affymetrix, aroma.cn, aroma.core |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | aroma.light_3.36.0.tar.gz |
| Windows Binary (x86_64) | aroma.light_3.36.0.zip |
| macOS Binary (x86_64) | aroma.light_3.36.0.tgz |
| macOS Binary (arm64) | aroma.light_3.36.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/aroma.light |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/aroma.light |
| Bioc Package Browser | https://code.bioconductor.org/browse/aroma.light/ |
| Package Short Url | https://bioconductor.org/packages/aroma.light/ |
| Package Downloads Report | Download Stats |