Last data update: 2014.03.03
Data Source
R Release (3.2.3)
CranContrib
BioConductor
All
Data Type
Packages
Functions
Images
Data set
Classification
Cran Task View
BiocViews
SMO (statistical methods ontology)
Results 1 - 10 of 169 found.
[1]
<
1
2
3
4
5
6
7
8
9
10
11
>
[17]
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
Sort:
-
Package Name ↑
Package Name ↓
Images
Functions
Datasets
Reverse Depends
Date
Package: mBPCR
Version: 1.26.0
Date: 2012-21-07
Title: Bayesian Piecewise Constant Regression for DNA copy number
estimation
Author: P.M.V. Rancoita <rancoita.paola@gmail.com>, with contributions
from M. Hutter <marcus.hutter@anu.edu.au>
Maintainer: P.M.V. Rancoita <rancoita.paola@gmail.com>
Description: Estimates the DNA copy number profile using mBPCR to
detect regions with copy number changes
Depends: oligoClasses , SNPchip
Imports: Biobase
Suggests: xtable
License: GPL (>= 2)
URL: http://www.idsia.ch/~paola/mBPCR
LazyData: yes
biocViews: aCGH, SNP, Microarray, CopyNumberVariation
NeedsCompilation: no
Packaged: 2016-05-04 03:16:45 UTC; biocbuild
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
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
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
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
● Data Source:
BioConductor
● BiocViews: AnnotationData, oligo
●
0 images,
1 functions ,
1 datasets
●
Reverse Depends: 0
Package: pd.hg18.60mer.expr
Title: Platform Design Info for NimbleGen hg18_60mer_expr
Description: Platform Design Info for NimbleGen hg18_60mer_expr
Version: 3.12.0
Author: Benilton Carvalho
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
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 23:35:53 UTC; benilton
● Data Source:
BioConductor
● BiocViews: AnnotationData, oligo
●
0 images,
1 functions ,
1 datasets
●
Reverse Depends: 0
Package: pd.ht.hg.u133.plus.pm
Title: Platform Design Info for The Manufacturer's Name
HT_HG-U133_Plus_PM
Description: Platform Design Info for The Manufacturer's Name HT_HG-U133_Plus_PM
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 23:37:09 UTC; benilton
● Data Source:
BioConductor
● BiocViews: AnnotationData, oligo
●
0 images,
1 functions ,
1 datasets
●
Reverse Depends: 0
Package: pd.ht.hg.u133a
Title: Platform Design Info for The Manufacturer's Name HT_HG-U133A
Description: Platform Design Info for The Manufacturer's Name HT_HG-U133A
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 23:39:12 UTC; benilton
● Data Source:
BioConductor
● BiocViews: AnnotationData, oligo
●
0 images,
1 functions ,
1 datasets
●
Reverse Depends: 0
Package: pd.ht.mg.430a
Title: Platform Design Info for The Manufacturer's Name HT_MG-430A
Description: Platform Design Info for The Manufacturer's Name HT_MG-430A
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 23:37:39 UTC; benilton
● Data Source:
BioConductor
● BiocViews: AnnotationData, oligo
●
0 images,
1 functions ,
1 datasets
●
Reverse Depends: 0
Package: pd.hta.2.0
Title: Platform Design Info for Affymetrix HTA-2_0
Description: Platform Design Info for Affymetrix HTA-2_0
Version: 3.12.1
Author: James W. MacDonald
Maintainer: James W. MacDonald <jmacdon@uw.edu>
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: 2015-11-17 21:39:33 UTC; jmacdon
● Data Source:
BioConductor
● BiocViews: AnnotationData, oligo
●
0 images,
1 functions ,
1 datasets
●
Reverse Depends: 0