R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
All

Data Type

Packages
Functions
Images
Data set

Classification

Results 1 - 4 of 4 found.
[1] < 1 > [1] Sort:

NSA : Post-normalization of total copy numbers

Package: NSA
Version: 0.0.32
Date: 2012-12-20
Title: Post-normalization of total copy numbers
Author: Maria Ortiz-Estevez <mortizest@gmail.com>, Ander Aranburu
<aaranburu@ceit.es>, Angel Rubio <arubio@ceit.es>
Maintainer: Maria Ortiz-Estevez <mortizest@gmail.com>
Depends: R (>= 2.11.1), R.methodsS3 (>= 1.2.0), MASS, matrixStats (>=
0.2.1), R.oo (>= 1.7.3), R.utils (>= 1.4.2), aroma.core (>=
1.6.0), aroma.affymetrix, DNAcopy
Description: Post-normalization of total copy-number estimates.
License: LGPL (>= 2.1)
URL: http://r-forge.r-project.org/projects/snpsprocessing/
LazyLoad: TRUE
biocViews: Infrastructure, Microarray, DNACopyNumber, Preprocessing,
aCGH, SNP, CopyNumberVariants
Repository: CRAN
Repository/R-Forge/Project: snpsprocessing
Repository/R-Forge/Revision: 202
Repository/R-Forge/DateTimeStamp: 2012-12-20 19:24:38
Date/Publication: 2012-12-21 09:17:05
Packaged: 2012-12-20 23:15:21 UTC; rforge

● Data Source: CranContrib
● BiocViews: CopyNumberVariants, DNACopyNumber, Infrastructure, Microarray, Preprocessing, SNP, aCGH
● 0 images, 11 functions, 0 datasets
● Reverse Depends: 0

aroma.affymetrix : Analysis of Large Affymetrix Microarray Data Sets

Package: aroma.affymetrix
Version: 3.0.0
Depends: R (>= 3.1.2), R.utils (>= 2.2.0), aroma.core (>= 3.0.0)
Imports: methods, R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0), R.cache (>=
0.12.0), R.devices (>= 2.13.2), R.filesets (>= 2.10.0),
aroma.apd (>= 0.6.0), MASS, splines, matrixStats (>= 0.50.1),
listenv, future
Suggests: DBI (>= 0.3.1), gsmoothr (>= 0.1.7), RColorBrewer (>= 1.1-2),
Biobase (>= 2.28.0), BiocGenerics (>= 0.14.0), affxparser (>=
1.40.0), affy (>= 1.46.0), affyPLM (>= 1.44.0), aroma.light (>=
2.4.0), gcrma (>= 2.40.0), limma (>= 3.24.1), oligo (>=
1.32.0), oligoClasses (>= 1.30.0), pdInfoBuilder (>= 1.32.0),
preprocessCore (>= 1.28.0), AffymetrixDataTestFiles, dChipIO
(>= 0.1.1)
SuggestsNote: BioC (>= 3.0), Recommended: preprocessCore, affyPLM,
aroma.light, affxparser, DNAcopy
Additional_repositories: http://r-forge.r-project.org
Date: 2016-01-09
Title: Analysis of Large Affymetrix Microarray Data Sets
Authors@R: c(
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email="henrikb@braju.com"),
person("James", "Bullard", role="ctb"),
person("Kasper", "Hansen", role="ctb"),
person("Pierre", "Neuvial", role="ctb"),
person("Elizabeth", "Purdom", role="ctb"),
person("Mark", "Robinson", role="ctb"),
person("Ken", "Simpson", role="ctb"))
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
License: LGPL (>= 2.1)
URL: http://www.aroma-project.org/
https://github.com/HenrikBengtsson/aroma.affymetrix
BugReports: https://github.com/HenrikBengtsson/aroma.affymetrix/issues
LazyLoad: TRUE
biocViews: Infrastructure, ProprietaryPlatforms, ExonArray, Microarray,
OneChannel, GUI, DataImport, DataRepresentation, Preprocessing,
QualityControl, Visualization, ReportWriting, aCGH,
CopyNumberVariants, DifferentialExpression, GeneExpression,
SNP, Transcription
NeedsCompilation: no
Packaged: 2016-01-09 21:38:52 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2016-01-10 00:00:03

● Data Source: CranContrib
● BiocViews: CopyNumberVariants, DataImport, DataRepresentation, DifferentialExpression, ExonArray, GUI, GeneExpression, Infrastructure, Microarray, OneChannel, Preprocessing, ProprietaryPlatforms, QualityControl, ReportWriting, SNP, Transcription, Visualization, aCGH
● 0 images, 331 functions, 0 datasets
● Reverse Depends: 2

aroma.cn : Copy-Number Analysis of Large Microarray Data Sets

Package: aroma.cn
Version: 1.6.1
Depends: R (>= 3.1.1), R.utils (>= 2.1.0), aroma.core (>= 2.14.0)
Imports: R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0), R.filesets (>=
2.9.0), R.cache (>= 0.10.0), matrixStats (>= 0.15.0), PSCBS (>=
0.50.0)
Suggests: aroma.light (>= 2.2.1), DNAcopy (>= 1.40.0), GLAD (>= 1.12.0)
SuggestsNote: BioC (>= 3.0), Recommended: aroma.light, DNAcopy
Date: 2015-10-27
Title: Copy-Number Analysis of Large Microarray Data Sets
Authors@R: c(
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email="henrikb@braju.com"),
person("Pierre", "Neuvial", role="aut"))
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.
License: LGPL (>= 2.1)
LazyLoad: TRUE
biocViews: ProprietaryPlatforms, aCGH, CopyNumberVariants, SNP,
Microarray, OneChannel, TwoChannel, DataImport,
DataRepresentation, Preprocessing, QualityControl
URL: http://www.aroma-project.org/
https://github.com/HenrikBengtsson/aroma.cn
BugReports: https://github.com/HenrikBengtsson/aroma.cn/issues
NeedsCompilation: no
Packaged: 2015-10-27 19:42:18 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2015-10-28 00:08:16

● Data Source: CranContrib
● BiocViews: CopyNumberVariants, DataImport, DataRepresentation, Microarray, OneChannel, Preprocessing, ProprietaryPlatforms, QualityControl, SNP, TwoChannel, aCGH
● 0 images, 29 functions, 0 datasets
● Reverse Depends: 0

calmate : Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

Package: calmate
Version: 0.12.1
Depends: R (>= 3.0.3), R.utils (>= 2.1.0), aroma.core (>= 2.14.0)
Imports: utils, MASS, R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0),
matrixStats (>= 0.14.2), R.filesets (>= 2.9.0)
Suggests: DNAcopy
Date: 2015-10-26
Title: Improved Allele-Specific Copy Number of SNP Microarrays for
Downstream Segmentation
Description: A multi-array post-processing method of allele-specific copy-number estimates (ASCNs).
Authors@R: c(
person("Maria", "Ortiz", role=c("aut", "ctb")),
person("Ander", "Aramburu", role=c("ctb")),
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email="henrikb@braju.com"),
person("Pierre", "Neuvial", role=c("aut", "ctb")),
person("Angel", "Rubio", role=c("aut", "ctb")))
License: LGPL (>= 2.1)
URL: https://github.com/HenrikBengtsson/calmate/
BugReports: https://github.com/HenrikBengtsson/calmate/issues
LazyLoad: TRUE
biocViews: aCGH, CopyNumberVariants, SNP, Microarray, OneChannel,
TwoChannel, Genetics
NeedsCompilation: no
Packaged: 2015-10-27 04:09:22 UTC; hb
Author: Maria Ortiz [aut, ctb],
Ander Aramburu [ctb],
Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut, ctb],
Angel Rubio [aut, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2015-10-27 08:09:53

● Data Source: CranContrib
● BiocViews: CopyNumberVariants, Genetics, Microarray, OneChannel, SNP, TwoChannel, aCGH
● 0 images, 9 functions, 0 datasets
● Reverse Depends: 0