aroma.cn-package: Package aroma.cn
In HenrikBengtsson/aroma.cn: Copy-Number Analysis of Large Microarray Data Sets
aroma.cn-package R Documentation
Package aroma.cn
Description
Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.
This package should be considered to be in an alpha or beta phase.
You should expect the API to be changing over time.
Installation and updates
To install this package, call install.packages("aroma.cn").
To get started
To get started, see:
...
License
The releases of this package is licensed under
LGPL version 2.1 or newer.
The development code of the packages is under a private licence
(where applicable) and patches sent to the author fall under the
latter license, but will be, if incorporated, released under the
"release" license above.
Author(s)
Henrik Bengtsson, Pierre Neuvial
References
Please cite PSCBS using one or more of the following references:
A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A. Olshen,
V.E. Seshan. Parent-specific copy number in paired tumor-normal
studies using circular binary segmentation, Bioinformatics, 2011
Please cite PSCBS using one or more of the following references:
H. Bengtsson, P. Neuvial and T.P. Speed. TumorBoost: Normalization of
allele-specific tumor copy numbers from a single pair of tumor-normal
genotyping microarrays, BMC Bioinformatics, 2010
H. Bengtsson, A. Ray, P. Spellman and T.P. Speed. A single-sample
method for normalizing and combining full-resolutioncopy numbers from
multiple platforms, labs and analysis methods, Bioinformatics, 2009
H. Bengtsson; K. Simpson; J. Bullard; K. Hansen. aroma.affymetrix: A
generic framework in R for analyzing small to very large Affymetrix
data sets in bounded memory, Tech Report 745, Department of Statistics,
University of California, Berkeley, February 2008
H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and
assessment of raw copy numbers at the single locus level,
Bioinformatics, 2008
To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.
HenrikBengtsson/aroma.cn documentation built on Feb. 20, 2024, 9:15 p.m.
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| aroma.cn-package | R Documentation |
Package aroma.cn
Description
Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.
This package should be considered to be in an alpha or beta phase. You should expect the API to be changing over time.
Installation and updates
To install this package, call install.packages("aroma.cn").
To get started
To get started, see:
...
License
The releases of this package is licensed under LGPL version 2.1 or newer.
The development code of the packages is under a private licence (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.
Author(s)
Henrik Bengtsson, Pierre Neuvial
References
Please cite PSCBS using one or more of the following references:
A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A. Olshen, V.E. Seshan. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation, Bioinformatics, 2011
Please cite PSCBS using one or more of the following references:
H. Bengtsson, P. Neuvial and T.P. Speed. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays, BMC Bioinformatics, 2010
H. Bengtsson, A. Ray, P. Spellman and T.P. Speed. A single-sample method for normalizing and combining full-resolutioncopy numbers from multiple platforms, labs and analysis methods, Bioinformatics, 2009
H. Bengtsson; K. Simpson; J. Bullard; K. Hansen. aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report 745, Department of Statistics, University of California, Berkeley, February 2008
H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008
To see these entries in BibTeX format, use 'print(<citation>, bibtex=TRUE)', 'toBibtex(.)', or set 'options(citation.bibtex.max=999)'.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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