R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 289 found.
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humanStemCell : Human Stem Cells time course experiment

Package: humanStemCell
Title: Human Stem Cells time course experiment
Version: 0.12.0
Author: R. Gentleman, N. Le Meur, M. Tewari
Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated).
biocViews: ExperimentData, Homo_sapiens_Data
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
License: Artistic-2.0
Depends: Biobase (>= 2.5.5), hgu133plus2.db
NeedsCompilation: no
Packaged: 2016-05-07 20:15:37 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: ExperimentData, Homo_sapiens_Data
● 0 images, 0 functions, 1 datasets
● Reverse Depends: 0

iBMQ : integrated Bayesian Modeling of eQTL data

Package: iBMQ
Type: Package
Title: integrated Bayesian Modeling of eQTL data
Version: 1.12.0
Date: 2011-10-28
Author: Marie-Pier Scott-Boyer and Greg Imholte
Maintainer: Greg Imholte <gimholte@uw.edu>
Description: integrated Bayesian Modeling of eQTL data
License: Artistic-2.0
Depends: R (>= 2.15.0), Biobase (>= 2.16.0), ggplot2 (>= 0.9.2)
biocViews: Microarray, Preprocessing, GeneExpression, SNP
URL: http://www.rglab.org
SystemRequirements: GSL and OpenMP
Packaged: 2016-05-04 04:47:55 UTC; biocbuild
NeedsCompilation: yes

● Data Source: BioConductor
● BiocViews: GeneExpression, Microarray, Preprocessing, SNP
● 0 images, 6 functions, 9 datasets
● Reverse Depends: 0

iCheck : QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

Package: iCheck
Type: Package
Title: QC Pipeline and Data Analysis Tools for High-Dimensional
Illumina mRNA Expression Data
Version: 1.2.0
Date: 2015-09-29
Author: Weiliang Qiu <stwxq@channing.harvard.edu>, Brandon Guo
<brandowonder@gmail.com> Christopher Anderson
<christopheranderson84@gmail.com>, Barbara Klanderman
<BKLANDERMAN@partners.org>, Vincent Carey
<stvjc@channing.harvard.edu>, Benjamin Raby
<rebar@channing.harvard.edu>
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
Depends: R (>= 3.2.0), Biobase, lumi, gplots
Imports: stats, graphics, preprocessCore, grDevices, randomForest,
affy, limma, parallel, vsn, GeneSelectMMD, rgl, MASS, lmtest,
scatterplot3d
Suggests:
biocViews: GeneExpression, DifferentialExpression, Microarray,
Preprocessing, DNAMethylation, OneChannel, TwoChannel,
QualityControl
Description: QC pipeline and data analysis tools for high-dimensional
Illumina mRNA expression data.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-05-04 06:34:08 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DNAMethylation, DifferentialExpression, GeneExpression, Microarray, OneChannel, Preprocessing, QualityControl, TwoChannel
● 8 images, 16 functions, 0 datasets
● Reverse Depends: 0

idiogram : idiogram

Package: idiogram
Version: 1.48.0
Title: idiogram
Description: A package for plotting genomic data by chromosomal location
Author: Karl J. Dykema <karl.dykema@vai.org>
Maintainer: Karl J. Dykema <karl.dykema@vai.org>
Depends: R (>= 2.10), methods, Biobase, annotate, plotrix
Suggests: hu6800.db, hgu95av2.db, golubEsets
License: GPL-2
ZipData: no
biocViews: Visualization
LazyData: yes
NeedsCompilation: no
Packaged: 2016-05-04 02:44:55 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Visualization
● 14 images, 4 functions, 2 datasets
● Reverse Depends: 1

inSilicoDb : Access to the InSilico Database

Package: inSilicoDb
Version: 2.7.0
Date: 2014-04-17
Title: Access to the InSilico Database
Description: Access expert curated and normalized microarray eSet datasets from the InSilico Database.
Authors@R:
c(person("Jaro", "Vanderheijden", email="jaro_vanderheijden@insilicodb.com", role="ctb"),
person("Quentin", "De Clerck", email="qdeclerc@vub.ac.be", role="ctb"),
person("Jonatan", "Taminau", email="jtaminau@gmail.com", role="cre"))
Maintainer: InSilico DB <support@insilicodb.com>
Depends: R (>= 3.0.0), rjson, Biobase, RCurl
Imports:
Suggests: limma
Collate: util.R interface.R basic.R
biocViews: Microarray, DataImport
License: GPL-2
URL: https://insilicodb.com
NeedsCompilation: no
Packaged: 2015-10-14 02:57:19 UTC; biocbuild
Author: Jaro Vanderheijden [ctb],
Quentin De Clerck [ctb],
Jonatan Taminau [cre]

● Data Source: BioConductor
● BiocViews: DataImport, Microarray
● 0 images, 14 functions, 0 datasets
● Reverse Depends: 0

inSilicoMerging : Collection of Merging Techniques for Gene Expression Data

Package: inSilicoMerging
Version: 1.15.0
Date: 2014-09-09
Title: Collection of Merging Techniques for Gene Expression Data
Description: Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies.
Authors@R:
c(person("Jaro", "Vanderheijden", email="jaro_vanderheijden@insilicodb.com", role="ctb"),
person("Quentin", "De Clerck", email="qdeclerc@vub.ac.be", role="ctb"),
person("Jonatan", "Taminau", email="jtaminau@gmail.com", role="cre"))
Maintainer: InSilico DB <support@insilicodb.com>
Depends: R (>= 2.11.1), Biobase
Suggests: BiocGenerics, inSilicoDb
Collate: util.R xpn.R merge.R mergeBMC.R mergeGENENORM.R mergeCOMBAT.R
mergeNONE.R mergeXPN.R color.R plotMDS.R plotRLE.R
plotGeneWiseBoxPlot.R test_inSilicoMerging_package.R
biocViews: Microarray
License: GPL-2
URL: http://insilicodb.com/
Packaged: 2015-10-14 03:30:53 UTC; biocbuild
NeedsCompilation: no
Author: Jaro Vanderheijden [ctb],
Quentin De Clerck [ctb],
Jonatan Taminau [cre]

● Data Source: BioConductor
● BiocViews: Microarray
● 0 images, 5 functions, 0 datasets
● Reverse Depends: 0

isobar : Analysis and quantitation of isobarically tagged MSMS proteomics data

Package: isobar
Title: Analysis and quantitation of isobarically tagged MSMS proteomics
data
Description: isobar provides methods for preprocessing, normalization, and
report generation for the analysis of quantitative mass spectrometry
proteomics data labeled with isobaric tags, such as iTRAQ and TMT.
Features modules for integrating and validating PTM-centric datasets
(isobar-PTM). More information on http://www.ms-isobar.org.
Version: 1.18.0
Author: Florian P Breitwieser <florian.bw@gmail.com> and
Jacques Colinge <jacques.colinge@inserm.fr>, with contributions from
Alexey Stukalov <stukalov@biochem.mpg.de>,
Xavier Robin <xavier.robin@unige.ch> and Florent Gluck <florent.gluck@unige.ch>
Maintainer: Florian P Breitwieser <florian.bw@gmail.com>
biocViews: Proteomics, MassSpectrometry, Bioinformatics,
MultipleComparisons, QualityControl
Depends: R (>= 2.10.0), Biobase, stats, methods
Imports: distr, plyr
Suggests: MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2, RJSONIO, Hmisc,
gplots, RColorBrewer, gridExtra, limma, boot, distr, DBI, MASS
LazyLoad: yes
License: LGPL-2
URL: https://github.com/fbreitwieser/isobar
BugReports: https://github.com/fbreitwieser/isobar/issues
Collate: utils.R ProteinGroup-class.R IBSpectra-class.R isobar-import.R
IBSpectra-plots.R NoiseModel-class.R Tlsd-class.R
ratio-methods.R distr-methods.R sharedpep-methods.R
report-utils-xls.R report-utils-tex.R report-utils.R
metareport-utils.R ptm-methods.R MSnSet-methods.R zzz.R
NeedsCompilation: no
Packaged: 2016-05-04 04:17:45 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Bioinformatics, MassSpectrometry, MultipleComparisons, Proteomics, QualityControl
● 7 images, 42 functions, 2 datasets
● Reverse Depends: 0

iterativeBMA : The Iterative Bayesian Model Averaging (BMA) algorithm

Package: iterativeBMA
Type: Package
Title: The Iterative Bayesian Model Averaging (BMA) algorithm
Version: 1.30.0
Date: 2009-7-22
Author: Ka Yee Yeung, University of Washington, Seattle, WA, with
contributions from Adrian Raftery and Ian Painter
Maintainer: Ka Yee Yeung <kayee@u.washington.edu>
Description: The iterative Bayesian Model Averaging (BMA) algorithm is
a variable selection and classification algorithm with an
application of classifying 2-class microarray samples, as
described in Yeung, Bumgarner and Raftery (Bioinformatics 2005,
21: 2394-2402).
Depends: BMA, leaps, Biobase (>= 2.5.5)
License: GPL (>= 2)
URL: http://faculty.washington.edu/kayee/research.html
biocViews: Microarray, Classification
NeedsCompilation: no
Packaged: 2016-05-04 03:09:23 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Classification, Microarray
● 1 images, 10 functions, 4 datasets
● Reverse Depends: 0

kidpack : DKFZ kidney package

Package: kidpack
Version: 1.14.0
Date: 16 September 2007
Title: DKFZ kidney package
Author: Wolfgang Huber <huber@ebi.ac.uk>
Depends: R (>= 2.6.0), Biobase (>= 2.5.5)
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
Description: kidney microarray data
License: GPL-2
URL: http://www.dkfz.de/mga
biocViews: ExperimentData, CancerData, KidneyCancerData,
MicroarrayData, ArrayExpress
NeedsCompilation: no
Packaged: 2016-05-07 20:11:54 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: ArrayExpress, CancerData, ExperimentData, KidneyCancerData, MicroarrayData
● 0 images, 0 functions, 2 datasets
● Reverse Depends: 0

leeBamViews : leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009

Package: leeBamViews
Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee
2009
Version: 1.8.0
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: data from PMID 19096707; prototype for managing multiple NGS samples
Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
Imports: GenomicRanges, GenomicAlignments, methods
Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR
Enhances: multicore
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic 2.0
LazyLoad: yes
biocViews: ExperimentData, Saccharomyces_cerevisiae_Data,
SequencingData, RNASeqData, SNPData
NeedsCompilation: no
Packaged: 2016-05-07 20:18:17 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: ExperimentData, RNASeqData, SNPData, Saccharomyces_cerevisiae_Data, SequencingData
● 0 images, 2 functions, 3 datasets
● Reverse Depends: 0