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Last data update: 2014.03.03

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Results 1 - 6 of 6 found.
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cqn : Conditional quantile normalization

Package: cqn
Version: 1.18.0
Title: Conditional quantile normalization
Description: A normalization tool for RNA-Seq data, implementing the
conditional quantile normalization method.
Author: Jean (Zhijin) Wu, Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore,
splines, quantreg
Imports: splines
Suggests: scales, edgeR
License: Artistic-2.0
LazyLoad: yes
biocViews: RNASeq, Preprocessing, DifferentialExpression
NeedsCompilation: no
Packaged: 2016-05-04 04:05:14 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DifferentialExpression, Preprocessing, RNASeq
● 1 images, 2 functions, 1 datasets
● Reverse Depends: 0

crlmm : Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

Package: crlmm
Type: Package
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Version: 1.30.0
Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
Ruczinski, Rafael A Irizarry
Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie
<mritchie@wehi.EDU.AU>
Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
arrays, as well as a copy number tool specific to 5.0, 6.0, and
Illumina platforms
License: Artistic-2.0
Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>=
1.17.7)
LinkingTo: preprocessCore (>= 1.17.7)
Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
matrixStats, VGAM, parallel
Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
RUnit
Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R
snprma-functions.R utils.R zzz.R test_crlmm_package.R
LazyLoad: yes
## Local Variables:
## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
## End:
biocViews: Microarray, Preprocessing, SNP, CopyNumberVariation
NeedsCompilation: yes
Packaged: 2016-05-04 03:14:37 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: CopyNumberVariation, Microarray, Preprocessing, SNP
● 3 images, 31 functions, 1 datasets
● Reverse Depends: 0

CopyNumber450k : R package for calling CNV from Illumina 450k methylation microarrays

Package: CopyNumber450k
Title: R package for calling CNV from Illumina 450k methylation
microarrays
Version: 1.8.0
Date: 2014-02-04
Author: Simon Papillon-Cavanagh, Jean-Philippe Fortin, Nicolas De Jay
Maintainer: Simon Papillon-Cavanagh
<simon.papillon-cavanagh@mail.mcgill.ca>
Description: This package contains a set of functions that allow CNV
calling from Illumina 450k methylation microarrays.
License: Artistic-2.0
Imports: methods
Depends: Biobase, minfi, DNAcopy, preprocessCore, BiocGenerics
Suggests: CopyNumber450kData, minfiData
LinkingTo:
LazyData: yes
Collate: AllClasses.R AllGenerics.R CNV450kSet-accessors.R
CNV450kSet-actions.R CNV450kSet-comparison.R
CNV450kSet-initialize.R CNV450kSet-plot.R extract.R
normalization.functional.R normalization.quantile.R
biocViews: DNAMethylation, Microarray, Preprocessing, QualityControl,
CopyNumberVariation
NeedsCompilation: no
Packaged: 2016-05-04 05:20:08 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: CopyNumberVariation, DNAMethylation, Microarray, Preprocessing, QualityControl
● 4 images, 1 functions, 0 datasets
● Reverse Depends: 0

AgiMicroRna : Processing and Differential Expression Analysis of Agilent microRNA chips

Package: AgiMicroRna
Version: 2.22.0
Title: Processing and Differential Expression Analysis of Agilent
microRNA chips
Author: Pedro Lopez-Romero <plopez@cnic.es>
Maintainer: Pedro Lopez-Romero <plopez@cnic.es>
Imports: Biobase
Depends: R (>= 2.10), methods, Biobase, limma, affy (>=
1.22), preprocessCore, affycoretools
Suggests: geneplotter, marray, gplots, gtools, gdata, codelink
LazyLoad: yes
Description: Processing and Analysis of Agilent microRNA data
License: GPL-3
biocViews: Microarray, AgilentChip, OneChannel, Preprocessing,
DifferentialExpression
NeedsCompilation: no
Packaged: 2016-05-04 03:18:23 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: AgilentChip, DifferentialExpression, Microarray, OneChannel, Preprocessing
● 19 images, 26 functions, 3 datasets
● Reverse Depends: 0

RefPlus : A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.

Package: RefPlus
Type: Package
Title: A function set for the Extrapolation Strategy (RMA+) and
Extrapolation Averaging (RMA++) methods.
Version: 1.42.0
Author: Kai-Ming Chang <kaiming@gmail.com>,
Chris Harbron <Chris.Harbron@astrazeneca.com>,
Marie C South <Marie.C.South@astrazeneca.com>
Maintainer: Kai-Ming Chang <kaiming@gmail.com>
Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM
(>= 1.18.0), preprocessCore (>= 1.4.0)
Suggests: affydata
Description: The package contains functions for pre-processing Affymetrix data
using the RMA+ and the RMA++ methods.
License: GPL (>= 2)
biocViews: Microarray, OneChannel, Preprocessing
NeedsCompilation: no
Packaged: 2016-05-04 02:57:30 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Microarray, OneChannel, Preprocessing
● 1 images, 6 functions, 0 datasets
● Reverse Depends: 0

affyPLM : Methods for fitting probe-level models

Package: affyPLM
Version: 1.48.0
Title: Methods for fitting probe-level models
Author: Ben Bolstad <bmb@bmbolstad.com>
Maintainer: Ben Bolstad <bmb@bmbolstad.com>
Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0),
Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1)
Imports: BiocGenerics, zlibbioc, graphics, grDevices, methods
Suggests: affydata, MASS
LinkingTo: preprocessCore
Description: A package that extends and improves the functionality of
the base affy package. Routines that make heavy use of
compiled code for speed. Central focus is on implementation of
methods for fitting probe-level models and tools using these
models. PLM based quality assessment tools.
License: GPL (>= 2)
URL: https://github.com/bmbolstad/affyPLM
biocViews: Microarray, OneChannel, Preprocessing, QualityControl
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-04 02:40:57 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Microarray, OneChannel, Preprocessing, QualityControl
● 5 images, 15 functions, 0 datasets
● Reverse Depends: 2