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Last data update: 2014.03.03

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Results 1 - 10 of 170 found.
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waveTiling : Wavelet-Based Models for Tiling Array Transcriptome Analysis

Package: waveTiling
Version: 1.14.0
Date: 2012-05-14
License: GPL (>=2)
Title: Wavelet-Based Models for Tiling Array Transcriptome Analysis
Author: Kristof De Beuf <kristof.debeuf@UGent.be>, Peter Pipelers
<peter.pipelers@ugent.be> and Lieven Clement
<lieven.clement@gmail.com>
Maintainer: Kristof De Beuf <kristof.debeuf@UGent.be>
Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs
Imports: methods, affy, preprocessCore, GenomicRanges, waveslim,
IRanges
Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData,
pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart22
Description: This package is designed to conduct transcriptome analysis
for tiling arrays based on fast wavelet-based functional
models.
Collate: allClasses.R allGenerics.R helperFunctions.R
initialize-methods.R methods-MapFilterProbe.R
methods-WaveTilingFeatureSet.R methods-WfmFit.R
methods-WfmInf.R show-methods.R
URL: https://r-forge.r-project.org/projects/wavetiling/
LazyLoad: yes
LazyData:
Packaged: 2016-05-04 04:40:22 UTC; biocbuild
biocViews: Microarray, DifferentialExpression, TimeCourse,
GeneExpression
NeedsCompilation: yes

● Data Source: BioConductor
● BiocViews: DifferentialExpression, GeneExpression, Microarray, TimeCourse
● 1 images, 27 functions, 0 datasets
● Reverse Depends: 0

puma : Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Package: puma
Type: Package
Title: Propagating Uncertainty in Microarray Analysis(including
Affymetrix tranditional 3' arrays and exon arrays and Human
Transcriptome Array 2.0)
Version: 3.14.0
Date: 2015-7-29
Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D.
Lawrence, Guido Sanguinetti, Li Zhang
Maintainer: Xuejun Liu <xuejun.liu@nuaa.edu.cn>
Depends: R (>= 3.2.0), oligo (>= 1.32.0), graphics, grDevices, methods,
stats, utils, mclust, oligoClasses
Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses
Suggests: pumadata, affydata, snow, limma, ROCR, annotate
Description: Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.
License: LGPL
biocViews: Microarray, OneChannel, Preprocessing,
DifferentialExpression, Clustering, ExonArray, GeneExpression,
mRNAMicroarray, ChipOnChip, AlternativeSplicing,
DifferentialSplicing, Bayesian, TwoChannel, DataImport, HTA2.0
URL: http://umber.sbs.man.ac.uk/resources/puma
Packaged: 2016-05-04 03:02:05 UTC; biocbuild
NeedsCompilation: yes

● Data Source: BioConductor
● BiocViews: AlternativeSplicing, Bayesian, ChipOnChip, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, ExonArray, GeneExpression, HTA2.0, Microarray, OneChannel, Preprocessing, TwoChannel, mRNAMicroarray
● 11 images, 53 functions, 8 datasets
● Reverse Depends: 1

pumadata : Various data sets for use with the puma package

Package: pumadata
Type: Package
Title: Various data sets for use with the puma package
Version: 2.8.0
Date: 2015-5-30
Author: Richard Pearson
Maintainer: Richard Pearson <richard.pearson@well.ox.ac.ukk>
Depends: R (>= 3.2.0), affy (>= 1.46.0), Biobase (>= 2.5.5), puma
, oligo (>= 1.32.0)
Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package.
License: LGPL
biocViews: ExperimentData, MicroarrayData, SNPData
URL: http://umber.sbs.man.ac.uk/resources/puma
Packaged: 2016-05-07 20:12:49 UTC; biocbuild
NeedsCompilation: no

● Data Source: BioConductor
● BiocViews: ExperimentData, MicroarrayData, SNPData
● 1 images, 0 functions, 23 datasets
● Reverse Depends: 0

pd.hg.u95e : Platform Design Info for The Manufacturer's Name HG_U95E

Package: pd.hg.u95e
Title: Platform Design Info for The Manufacturer's Name HG_U95E
Description: Platform Design Info for The Manufacturer's Name HG_U95E
Version: 3.12.0
Author: Benilton Carvalho
Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com>
LazyLoad: yes
Depends: R (>= 3.2.0), Biostrings (>= 2.35.12), methods, RSQLite (>=
1.0.0), oligoClasses (>= 1.29.6), oligo (>= 1.31.5), DBI (>=
0.3.1), IRanges (>= 2.1.43), S4Vectors (>= 0.5.22)
License: Artistic-2.0
biocViews: AnnotationData, oligo
ZipData: no
NeedsCompilation: no
Packaged: 2015-04-12 23:40:06 UTC; benilton