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webbioc : Bioconductor Web Interface

Package: webbioc
Version: 1.44.0
Date: 2009-02-05
Title: Bioconductor Web Interface
Author: Colin A. Smith <colin@colinsmith.org>
Maintainer: Colin A. Smith <colin@colinsmith.org>
Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma,
qvalue
Imports: multtest, qvalue, stats, utils, BiocInstaller
SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm
Description: An integrated web interface for doing microarray analysis
using several of the Bioconductor packages. It is intended to
be deployed as a centralized bioinformatics resource for use
by many users. (Currently only Affymetrix oligonucleotide
analysis is supported.)
License: GPL (>= 2)
URL: http://www.bioconductor.org/
LazyLoad: yes
biocViews: Infrastructure, Microarray, OneChannel,
DifferentialExpression
NeedsCompilation: no
Packaged: 2016-05-04 02:39:29 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DifferentialExpression, Infrastructure, Microarray, OneChannel
● 0 images, 2 functions, 0 datasets
● Reverse Depends: 0

MmPalateMiRNA : Murine Palate miRNA Expression Analysis

Package: MmPalateMiRNA
Type: Package
Title: Murine Palate miRNA Expression Analysis
Version: 1.22.0
Date: 2012-11-06
Author: Guy Brock <guy.brock@louisville.edu>, Partha Mukhopadhyay
<p0mukh01@louisville.edu>, Vasyl Pihur
<vasyl.pihur@louisville.edu>, Robert M. Greene
<Dr.Bob.Greene@gmail.com>, and M. Michele Pisano
<mmpisa01@louisville.edu>
Maintainer: Guy Brock <guy.brock@louisville.edu>
Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod,
lattice, vsn
Imports: limma, lattice, Biobase
Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA,
targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid,
class, cluster, multtest, RColorBrewer, latticeExtra
Description: R package compendium for the analysis of murine palate
miRNA two-color expression data.
License: GPL-3
LazyLoad: yes
Collate: MmPalateMiRNA-Methods.R MmPalateMiRNA-functions.R
Packaged: 2016-05-04 04:17:31 UTC; biocbuild
biocViews: Microarray, TwoChannel, QualityControl, Preprocessing,
DifferentialExpression, MultipleComparison, Clustering, GO,
Pathways, ReportWriting, SequenceMatching
NeedsCompilation: no

● Data Source: BioConductor
● BiocViews: Clustering, DifferentialExpression, GO, Microarray, MultipleComparison, Pathways, Preprocessing, QualityControl, ReportWriting, SequenceMatching, TwoChannel
● 5 images, 12 functions, 1 datasets
● Reverse Depends: 0

cellHTS2 : Analysis of cell-based screens - revised version of cellHTS

Package: cellHTS2
Version: 2.36.0
Title: Analysis of cell-based screens - revised version of cellHTS
Author: Ligia Bras, Wolfgang Huber <whuber@embl.de>, Michael Boutros <m.boutros@dkfz.de>, Gregoire Pau <gpau@embl.de>, Florian Hahne <florian.hahne@novartis.com>
Maintainer: Joseph Barry <joseph.barry@embl.de>
Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter,
splots, vsn, hwriter, locfit, grid
Suggests: ggplot2
Imports: prada, GSEABase, Category, stats4
Description: This package provides tools for the analysis of high-throughput assays that were performed in microtitre plate formats (including but not limited to 384-well plates). The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries. See ?cellHTS2 for a brief introduction.
Reference: Michael Boutros and Ligia P. Bras and Wolfgang Huber.
Analysis of cell-based RNAi screens. Genome Biology 7:7 R66
(2006).
License: Artistic-2.0
URL: http://www.dkfz.de/signaling
biocViews: CellBasedAssays, Preprocessing, Visualization
Collate: AllClasses.R AllGenerics.R adjustVariance.R checkColumns.R
checkControls.R convertOldCellHTS.R envisionPlateReader.R
getDynamicRange.R getMeasureRepAgreement.R getTopTable.R
getZfactor.R gseaModule.R glossary.R htmlFunctions.R
imageScreen.R makePlot.R methods-cellHTS.R methods-ROC.R
normalizePlates.R oneRowPerId.R perPlateScaling.R
plateConfModule.R plateListModule.R plateSummariesModule.R
plotSpatialEffects.R progressReport.R readHTAnalystData.R
readPlateList.R rsa.R screenResultsModule.R
screenDescriptionModule.R screenScriptModule.R
screenSummaryModule.R settings.R summarizeReplicates.R
tableOutput.R templateDescriptionFile.R writeHTML-methods.R
writeReport.R write.tabdel.R zzz.R
NeedsCompilation: no
Packaged: 2016-05-04 03:03:58 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: CellBasedAssays, Preprocessing, Visualization
● 6 images, 42 functions, 5 datasets
● Reverse Depends: 3

affyPara : Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Package: affyPara
Version: 1.32.0
Title: Parallelized preprocessing methods for Affymetrix
Oligonucleotide Arrays
Date: 2013-03-25
Author: Markus Schmidberger <schmidb@ibe.med.uni-muenchen.de>, Esmeralda Vicedo <e.vicedo@gmx.net>, Ulrich Mansmann <mansmann@ibe.med.uni-muenchen.de>
Maintainer: Markus Schmidberger <MSchmidberger@freenet.de>
Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn
(>= 3.6.0), aplpack (>= 1.1.1), affyio
Suggests: affydata
Enhances: affy
Description: The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.
biocViews: Microarray, Preprocessing
Reference: M. Schmidberger, U. Mansmann; Parallelized preprocessing
algorithms for high-density oligonucleotide array data; 22th
International Parallel and Distributed Processing Symposium
(IPDPS 2008), Proceedings, 14-18 April 2008, Miami, Florida,
USA. IEEE 2008 (http://www.hicomb.org/papers/HICOMB2008-03.pdf)
License: GPL-3
URL: http://www.ibe.med.uni-muenchen.de
NeedsCompilation: no
Packaged: 2016-05-04 03:06:46 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Microarray, Preprocessing
● 0 images, 20 functions, 0 datasets
● Reverse Depends: 0