Package: ABarray Version: 1.4.2 Depends: Biobase, multtest Suggests: limma, LPE Title: Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. Description: Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used. biocViews: Microarray, OneChannel, Preprocessing Author: Yongming Andrew Sun Maintainer: Yongming Andrew Sun License: GPL source.ver: src/contrib/ABarray_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.5/ABarray_1.4.2.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ABarray_1.4.2.tgz vignettes: vignettes/ABarray/inst/doc/ABarray.pdf, vignettes/ABarray/inst/doc/ABarrayGUI.pdf Package: ACME Version: 1.2.1 Depends: R (>= 2.4.0), methods Title: Algorithms for Calculating Microarray Enrichment (ACME) Description: ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. biocViews: Statistics Author: Sean Davis Maintainer: Sean Davis URL: None License: GPL version 2 or newer source.ver: src/contrib/ACME_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/ACME_1.2.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ACME_1.2.1.tgz vignettes: vignettes/ACME/inst/doc/ACME.pdf Package: AnnBuilder Version: 1.14.0 Depends: R (>= 2.1.0), methods, Biobase, XML, annotate, utils Suggests: RSQLite, RCurl, GO Title: Bioconductor annotation data package builder Description: Processing annotation date from public data repositories and building annoation data packages or XML data documents using the source data. biocViews: Annotation, Microarray Author: J. Zhang Maintainer: J. Zhang License: LGPL source.ver: src/contrib/AnnBuilder_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/AnnBuilder_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/AnnBuilder_1.14.0.tgz vignettes: vignettes/AnnBuilder/inst/doc/ABPrimer.pdf, vignettes/AnnBuilder/inst/doc/AnnBuilder.pdf Package: BSgenome Version: 1.4.1 Depends: R (>= 2.5.0), methods, Biobase (>= 1.14.0), Biostrings (>= 2.4.7) Suggests: BSgenome.Celegans.UCSC.ce2 Title: Infrastructure for Biostrings-based genome data packages Description: Infrastructure shared by all the Biostrings-based genome data packages biocViews: Genetics, Infrastructure Author: Herve Pages Maintainer: H. Pages License: LGPL source.ver: src/contrib/BSgenome_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/BSgenome_1.4.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/BSgenome_1.4.1.tgz Package: BeadExplorer Version: 1.2.0 Depends: R (>= 2.4.0), widgetTools, affy, R2HTML, grDevices, tkWidgets, methods Title: QC, normalisation, annotation and exploration of Illumina BeadChip data Description: QC, normalisation, annotation and exploration of Illumina BeadChip data biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Transcription, DataImport, Statistics, DifferentialExpression Author: Gareth Elvidge Maintainer: Gareth Elvidge License: GPL (version 2 or newer) source.ver: src/contrib/BeadExplorer_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/BeadExplorer_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/BeadExplorer_1.2.0.tgz vignettes: vignettes/BeadExplorer/inst/doc/BeadHelp.pdf Package: BioMVCClass Version: 1.4.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz Title: Model-View-Controller (MVC) Classes That Use Biobase Description: Creates classes used in model-view-controller (MVC) design biocViews: Visualization, Infrastructure, GraphsAndNetworks Author: Elizabeth Whalen Maintainer: Elizabeth Whalen License: LGPL source.ver: src/contrib/BioMVCClass_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/BioMVCClass_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/BioMVCClass_1.4.0.tgz vignettes: vignettes/BioMVCClass/inst/doc/BioMVCClass.pdf Package: Biobase Version: 1.14.1 Depends: R (>= 2.5.0), tools, methods, utils Suggests: tkWidgets Title: Biobase: Base functions for Bioconductor Description: Functions that are needed by many other packages or which replace R functions. biocViews: Infrastructure, Statistics Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/Biobase_1.14.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/Biobase_1.14.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Biobase_1.14.1.tgz vignettes: vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf, vignettes/Biobase/inst/doc/Bioconductor.pdf, vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf, vignettes/Biobase/inst/doc/HowTo.pdf, vignettes/Biobase/inst/doc/esApply.pdf Package: Biostrings Version: 2.4.8 Depends: R (>= 2.5.0), methods Suggests: RUnit, BSgenome, BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.FlyBase.r51, hgu95av2probe Title: String objects representing biological sequences, and matching algorithms Description: Class definitions and generics for biological sequences along with pattern matching algorithms. biocViews: SequenceMatching, Genetics, Infrastructure Author: H. Pages, R. Gentleman and S. DebRoy Maintainer: H. Pages License: LGPL source.ver: src/contrib/Biostrings_2.4.8.tar.gz win.binary.ver: bin/windows/contrib/2.5/Biostrings_2.4.8.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Biostrings_2.4.8.tgz vignettes: vignettes/Biostrings/inst/doc/Alignments.pdf, vignettes/Biostrings/inst/doc/Biostrings2Classes.pdf, vignettes/Biostrings/inst/doc/DNAStringVectorization.pdf, vignettes/Biostrings/inst/doc/matchPattern.pdf Package: BufferedMatrixMethods Version: 1.0.0 Depends: R (>= 2.4.0), BufferedMatrix (>= 0.1.20) Title: Microarray Data related methods that utlize BufferedMatrix objects Description: Microarray analysis methods that use BufferedMatrix objects biocViews: Infrastructure Author: B. M. Bolstad Maintainer: B. M. Bolstad URL: http://www.bmbolstad.com License: GPL version 2 or later source.ver: src/contrib/BufferedMatrixMethods_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/BufferedMatrixMethods_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/BufferedMatrixMethods_1.0.0.tgz Package: BufferedMatrix Version: 1.0.1 Depends: methods Title: A matrix data storage object held in temporary files Description: A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data. biocViews: Infrastructure Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad License: LGPL version 2 or newer source.ver: src/contrib/BufferedMatrix_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/BufferedMatrix_1.0.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/BufferedMatrix_1.0.0.tgz vignettes: vignettes/BufferedMatrix/inst/doc/BufferedMatrix.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture1.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture2.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture3.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture4.pdf, vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture5.pdf Package: CALIB Version: 1.2.0 Depends: limma, methods Title: Calibration model for estimating absolute expression levels from microarray data Description: This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estiamted from external control spikes. biocViews: Microarray,TwoChannel,Preprocessing Author: Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal Maintainer: Hui Zhao License: LGPL source.ver: src/contrib/CALIB_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/CALIB_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/CALIB_1.2.0.tgz vignettes: vignettes/CALIB/inst/doc/quickstart.pdf, vignettes/CALIB/inst/doc/readme.pdf Package: CORREP Version: 1.2.0 Depends: e1071 Suggests: cluster Title: Multivariate Correlation Estimator and Statistical Inference Procedures. Description: Multivariate correlation estimation and statistical inference. See package vignette. biocViews: Statistics, Microarray, Clustering, GraphsAndNetworks Author: Dongxiao Zhu and Youjuan Li Maintainer: Dongxiao Zhu License: GPL 2.0 or newer source.ver: src/contrib/CORREP_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/CORREP_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/CORREP_1.2.0.tgz vignettes: vignettes/CORREP/inst/doc/CORREP.pdf Package: Category Version: 2.2.3 Depends: methods, Biobase (>= 1.13.37), graph, KEGG, GO, annotate (>= 1.13.7), genefilter, Matrix Imports: methods, Biobase (>= 1.13.37), RBGL Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-3), hgu95av2 Title: Category Analysis Description: A collection of tools for performing category analysis. biocViews: Statistics, Annotation, GO, Pathways Author: R. Gentleman with contributions from S. Falcon Maintainer: S. Falcon License: The Artistic License, Version 2.0 source.ver: src/contrib/Category_2.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.5/Category_2.2.3.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Category_2.2.3.tgz vignettes: vignettes/Category/inst/doc/Category.pdf Package: ChromoViz Version: 1.8.0 Depends: RSvgDevice, XML Title: Multimodal visualization of gene expression data Description: Draw gene expression profile along with annotation data onto chromosome using SVG(Scalable Vector Graphics) biocViews: Annotation, Visualization, Microarray Author: Jihoon Kim Maintainer: Jihoon Kim License: GPL source.ver: src/contrib/ChromoViz_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/ChromoViz_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ChromoViz_1.8.0.tgz Package: CoCiteStats Version: 1.8.0 Depends: R (>= 2.0), humanLLMappings Title: Different test statistics based on co-citation. Description: A collection of software tools for dealing with co-citation data. biocViews: Statistics Author: B. Ding and R. Gentleman Maintainer: R. Gentleman License: CPL source.ver: src/contrib/CoCiteStats_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/CoCiteStats_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/CoCiteStats_1.8.0.tgz Package: DEDS Version: 1.8.0 Depends: R (>= 1.7.0), methods Title: Differential Expression via Distance Summary for Microarray Data Description: This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach. biocViews: Statistics, Microarray, DifferentialExpression Author: Yuanyuan Xiao , Jean Yee Hwa Yang Maintainer: Yuanyuan Xiao License: LGPL source.ver: src/contrib/DEDS_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/DEDS_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/DEDS_1.8.0.tgz vignettes: vignettes/DEDS/inst/doc/DEDS.pdf Package: DNAcopy Version: 1.10.0 Title: DNA copy number data analysis Description: Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number biocViews: Microarray, DNACopyNumber Author: E. S. Venkatraman & Adam Olshen Maintainer: E. S. Venkatraman License: GPL version 2 or later source.ver: src/contrib/DNAcopy_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/DNAcopy_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/DNAcopy_1.10.0.tgz vignettes: vignettes/DNAcopy/inst/doc/DNAcopy.pdf Package: DynDoc Version: 1.14.0 Depends: methods, utils Imports: methods Title: Dynamic document tools Description: A set of functions to create and interact with dynamic documents and vignettes. biocViews: ReportWriting Author: R. Gentleman, Jeff Gentry Maintainer: Biocore Team License: Artistic License, Version 2.0 source.ver: src/contrib/DynDoc_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/DynDoc_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/DynDoc_1.14.0.tgz Package: EBImage Version: 2.0.1 Depends: R (>= 2.4.0), methods, utils Title: Image processing and analysis toolkit for R Description: The package provides functionality to perform image processing and image analysis in R. It was originally designed to support automated image analysis in high throughput cell-based microscopy assay and is being largerly developed in that direction. However, the package is of general natuare and can be used for other problems that require image analysis. The package supports over 95 image formats through its interface to ImageMagick and provides functions standard image filters plus morphological transformations and object detection algroithms. It has a build-in image viewer which supports single images and image stacks. biocViews: Visualization Author: Oleg Sklyar, Wolfgang Huber Maintainer: Oleg Sklyar URL: http://www.ebi.ac.uk/~osklyar/EBImage/ License: LGPL SystemRequirements: ImageMagick (> 6.1.7), GTK+ (> 2.6) -- Windows dependencies are available from the URL below! See package vignette for installation instructions. source.ver: src/contrib/EBImage_2.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/EBImage_2.0.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/EBImage_2.0.1.tgz vignettes: vignettes/EBImage/inst/doc/AnalysisWithEBImage.pdf, vignettes/EBImage/inst/doc/EBImageInstallHOWTO.pdf Package: EBarrays Version: 1.8.1 Depends: R (>= 2.4.0), Biobase (>= 1.11.0), methods, utils, lattice Title: Empirical Bayes for Microarrays Description: EBarrays provides tools for the analysis of replicated microarray data across multiple conditions. biocViews: Statistics, DifferentialExpression, Microarray Author: Christina Kendziorski, Michael Newton and Deepayan Sarkar Maintainer: Deepayan Sarkar License: GPL Version 2.0 or later. source.ver: src/contrib/EBarrays_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/EBarrays_1.8.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/EBarrays_1.8.1.tgz vignettes: vignettes/EBarrays/inst/doc/vignette.pdf Package: GEOquery Version: 2.0.6 Depends: methods Suggests: limma,Biobase Title: Get data from NCBI Gene Expression Omnibus (GEO) Description: The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data (>150,000 experiments). Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor. biocViews: Microarray, DataImport, OneChannel, TwoChannel, SAGE Author: Sean Davis Maintainer: Sean Davis License: GPL version 2 source.ver: src/contrib/GEOquery_2.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.5/GEOquery_2.0.6.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GEOquery_2.0.6.tgz vignettes: vignettes/GEOquery/inst/doc/GEOquery.pdf Package: GGtools Version: 1.4.0 Depends: R (>= 2.2.0), methods, Biobase (>= 1.11.26), hgfocus, geneplotter(>= 1.11.8), mgu74av2 Title: software and data for genetical genomics (c) 2006 VJ Carey Description: dealing with hapmap SNP reports, GWAS, etc. biocViews: SNPsAndGeneticVariability, Genetics, Statistics Author: Vince Carey Maintainer: Vince Carey License: Artistic (see COPYING) source.ver: src/contrib/GGtools_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GGtools_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GGtools_1.4.0.tgz vignettes: vignettes/GGtools/inst/doc/GGOverview-dosc.pdf, vignettes/GGtools/inst/doc/GGoverview.pdf Package: GLAD Version: 1.10.0 Depends: R (>= 1.8.0), aws Title: Gain and Loss Analysis of DNA Description: Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified. biocViews: Microarray, DNACopyNumber Author: Philippe Hupe Maintainer: Philippe Hupe URL: http://bioinfo.curie.fr License: GPL source.ver: src/contrib/GLAD_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GLAD_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GLAD_1.10.0.tgz vignettes: vignettes/GLAD/inst/doc/GLAD.pdf Package: GOstats Version: 2.2.6 Depends: graph (>= 1.13.10), GO (>= 1.13.0), annotate (>= 1.13.2), RBGL, Biobase (>= 1.11.42), Category (>= 2.2.3), methods Imports: Biobase (>= 1.11.42), Category (>= 2.2.3), methods Suggests: hgu95av2 (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, Rgraphviz, xtable, SparseM Title: Tools for manipulating GO and microarrays. Description: A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations. biocViews: Statistics, Annotation, GO, MultipleComparisons Author: R. Gentleman and S. Falcon Maintainer: S. Falcon License: The Artistic License, Version 2.0 source.ver: src/contrib/GOstats_2.2.6.tar.gz win.binary.ver: bin/windows/contrib/2.5/GOstats_2.2.6.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GOstats_2.2.6.tgz vignettes: vignettes/GOstats/inst/doc/GOstatsHyperG.pdf, vignettes/GOstats/inst/doc/GOvis.pdf Package: GeneMeta Version: 1.8.0 Depends: R (>= 2.4), methods, Biobase (>= 1.11.34), genefilter Imports: methods, Biobase (>= 1.11.34) Title: MetaAnalysis for High Throughput Experiments Description: A collection of meta-analysis tools for analysing high throughput experimental data biocViews: Statistics Author: Lara Lusa , R. Gentleman, M. Ruschhaupt Maintainer: Biocore Team License: Artistic License, Version 2.0 source.ver: src/contrib/GeneMeta_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GeneMeta_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GeneMeta_1.8.0.tgz vignettes: vignettes/GeneMeta/inst/doc/GeneMeta.pdf Package: GeneR Version: 2.6.0 Title: R for genes and sequences analysis Description: Package manipulating nucleotidic sequences (Embl, Fasta, GenBank) biocViews: Annotation, Genetics Author: L. Cottret, A. Lucas, E. Marrakchi, O. Rogier, V. Lefort, P. Durosay, A. Viari, C. Thermes & Y. d'Aubenton-Carafa. Maintainer: Y. d'Aubenton-Carafa URL: http://www.cgm.cnrs-gif.fr License: Free Software Licence CeCILL source.ver: src/contrib/GeneR_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GeneR_2.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GeneR_2.6.0.tgz vignettes: vignettes/GeneR/inst/doc/GeneR.pdf, vignettes/GeneR/inst/doc/GeneR_address.pdf Package: GeneSpring Version: 2.10.0 Depends: R (>= 2.0.1), Biobase (>= 1.5.0), methods Title: GeneSpring R Integration Functions Description: Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects biocViews: Infrastructure Author: Thon de Boer Maintainer: Thon de Boer URL: http://www.chem.agilent.com/scripts/generic.asp?lpage=34733 License: GPL source.ver: src/contrib/GeneSpring_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GeneSpring_2.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GeneSpring_2.10.0.tgz vignettes: vignettes/GeneSpring/inst/doc/GeneSpring.pdf Package: GeneTS Version: 2.14.0 Depends: R (>= 2.0.0), GeneCycle (>= 1.0.0), GeneNet (>= 1.0.0) Title: Microarray Time Series and Network Analysis Description: With the present version, GeneTS has become a meta-package that exists mainly for reasons of backward compatibility. Its only purpose is to load the GeneCycle and GeneNet packages.You may load either of these packages directly. biocViews: TimeCourse, GraphsAndNetworks, MultipleComparisons, Visualization Author: Miika Ahdesmaki, Konstantinos Fokianos, Rainer Opgen-Rhein, Juliane Schaefer, and Korbinian Strimmer. Maintainer: Korbinian Strimmer URL: http://www.strimmerlab.org/software/genets/ License: GPL version 2 or newer source.ver: src/contrib/GeneTS_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GeneTS_2.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GeneTS_2.14.0.tgz Package: GeneTraffic Version: 1.8.0 Depends: R (>= 1.8.1), Biobase (>= 1.4.0), affy (>= 1.3.28), marray (>= 1.5.10), SSOAP(>= 0.1.2), XML (>= 0.95.6), digest(>= 0.1.1), methods Title: GeneTraffic R Integration Functions Description: Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's exprSet, for 2 color projects marray's marrayRaw) biocViews: Infrastructure, Microarray Author: Daniel Iordan Maintainer: Daniel Iordan URL: http://www.iobion.com/web_services/GeneTrafficAPI/ License: GPL source.ver: src/contrib/GeneTraffic_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GeneTraffic_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GeneTraffic_1.8.0.tgz vignettes: vignettes/GeneTraffic/inst/doc/GeneTraffic.pdf Package: GeneticsBase Version: 1.0.0 Depends: R (>= 2.3.1), methods, combinat, xtable, mvtnorm Imports: combinat, gdata (>= 2.3.0), gplots (>= 2.3.1), gtools (>= 2.2.3), MASS, haplo.stats (>= 1.2.2) Title: Classes and functions for handling genetic data Description: The R Genetics Project is a collaborative effort to develop a complete set of tools for storing, accessing, manipulating, and analyzing genetics data, from small candidate-gene studies consisting of a few genetic markers to large whole-genome studies containing hundreds of thousands of markers. This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions. biocViews: Genetics Author: Gregory Warnes Ross Lazarus Scott D Chasalow Giovanni Montana Michael O'Connell Junsheng Cheng Nitin Jain Maintainer: Gregory Warnes License: LGPL source.ver: src/contrib/GeneticsBase_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GeneticsBase_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GeneticsBase_1.0.0.tgz vignettes: vignettes/GeneticsBase/inst/doc/CAMP_LD_html.pdf, vignettes/GeneticsBase/inst/doc/CAMP_alleleSummary_html.pdf, vignettes/GeneticsBase/inst/doc/CAMP_genotypeSummary_html.pdf, vignettes/GeneticsBase/inst/doc/SummaryTables.pdf Package: GeneticsDesign Version: 1.0.0 Depends: combinat, gdata, mvtnorm Title: Functions for designing genetics studies Description: This package contains functions useful for designing genetics studies, including power and sample-size calculations. biocViews: Genetics Author: Gregory Warnes David Duffy , Michael Man Weiliang Qiu Ross Lazarus Maintainer: Weiliang Qiu License: GPL source.ver: src/contrib/GeneticsDesign_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GeneticsDesign_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GeneticsDesign_1.0.0.tgz vignettes: vignettes/GeneticsDesign/inst/doc/GPC.pdf Package: GeneticsPed Version: 1.0.0 Depends: R (>= 2.4.0), gdata (>= 2.3.0), MASS Title: Pedigree and genetic relationship functions Description: Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities biocViews: Genetics Author: Gregor Gorjanc and David A. Henderson , with code contributions by Brian Kinghorn and Andrew Percy (see file COPYING) Maintainer: Gregor Gorjanc URL: http://rgenetics.org License: LGPL version 2.1 or later source.ver: src/contrib/GeneticsPed_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GeneticsPed_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GeneticsPed_1.0.0.tgz vignettes: vignettes/GeneticsPed/inst/doc/geneticRelatedness.pdf, vignettes/GeneticsPed/inst/doc/pedigreeHandling.pdf, vignettes/GeneticsPed/inst/doc/quanGenAnimalModel.pdf Package: GlobalAncova Version: 3.2.0 Depends: methods, corpcor, globaltest Imports: annotate Suggests: Biobase, GO, multtest, golubEsets, hu6800, hgu133a, vsn Title: Calculates a global test for differential gene expression between groups Description: We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany. biocViews: Microarray, OneChannel, Statistics, DifferentialExpression, Pathways Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele Maintainer: R. Meister License: GPL Version 2 or newer source.ver: src/contrib/GlobalAncova_3.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GlobalAncova_3.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GlobalAncova_3.2.0.tgz vignettes: vignettes/GlobalAncova/inst/doc/GlobalAncova.pdf, vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.pdf Package: GraphAT Version: 1.8.0 Depends: MCMCpack, graph Title: Graph Theoretic Association Tests Description: Functions and data used in Balasubramanian, et al. (2004) biocViews: Statistics, GraphsAndNetworks Author: R. Balasubramanian, T. LaFramboise, D. Scholtens Maintainer: Thomas LaFramboise License: LGPL source.ver: src/contrib/GraphAT_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/GraphAT_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/GraphAT_1.8.0.tgz Package: HEM Version: 1.8.0 Depends: R (>= 2.1.0), Biobase Title: Heterogeneous error model for identification of differentially expressed genes under multiple conditions Description: This package fits heterogeneous error models for analysis of microarray data biocViews: Microarray, DifferentialExpression, Statistics Author: HyungJun Cho and Jae K. Lee Maintainer: HyungJun Cho URL: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ License: GPL version 2 or newer source.ver: src/contrib/HEM_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/HEM_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/HEM_1.8.0.tgz vignettes: vignettes/HEM/inst/doc/HEM.pdf Package: Harshlight Version: 1.4.0 Depends: R (>= 2.1.1), affy Title: A "corrective make-up" program for microarray chips Description: The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned. The defective areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. biocViews: Microarray, QualityControl, Preprocessing Author: Mayte Suarez-Farinas, Maurizio Pellegrino, Knut W. Mittkowsky, Marcelo O. Magnasco. Maintainer: Maurizio Pellegrino URL: http://asterion.rockefeller.edu/Harshlight/ License: GPL version 2 or later source.ver: src/contrib/Harshlight_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/Harshlight_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Harshlight_1.4.0.tgz vignettes: vignettes/Harshlight/inst/doc/Harshlight.pdf Package: Heatplus Version: 1.6.0 Title: A heat map displaying covariates and coloring clusters Description: Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display. biocViews: Microarray, Visualization Author: Alexander Ploner Maintainer: Alexander Ploner License: GPL 2 or later source.ver: src/contrib/Heatplus_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/Heatplus_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Heatplus_1.6.0.tgz vignettes: vignettes/Heatplus/inst/doc/Heatplus.pdf Package: Icens Version: 1.8.0 Depends: survival Title: NPMLE for Censored and Truncated Data Description: Many functions for computing the NPMLE for censored and truncated data. biocViews: Statistics, TimeCourse Author: R. Gentleman and Alain Vandal . Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/Icens_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/Icens_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Icens_1.8.0.tgz Package: KEGGSOAP Version: 1.10.0 Depends: methods, XML, SSOAP (>= 0.2-2), RCurl (>= 0.4) Imports: SSOAP (>= 0.2-2) Title: Client-side SOAP access KEGG Description: A package that provides a client interface to the KEGG SOAP server biocViews: Annotation, Pathways Author: J. Zhang and R. Gentleman Maintainer: J. Zhang License: BSD source.ver: src/contrib/KEGGSOAP_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/KEGGSOAP_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/KEGGSOAP_1.10.0.tgz Package: LBE Version: 1.4.0 Suggests: qvalue Title: Estimation of the false discovery rate. Description: LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. biocViews: Statistics, MultipleComparisons Author: Cyril Dalmasso Maintainer: Cyril Dalmasso License: GPL 2 source.ver: src/contrib/LBE_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/LBE_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/LBE_1.4.0.tgz vignettes: vignettes/LBE/inst/doc/LBE.pdf Package: LMGene Version: 1.6.0 Depends: R (>= 2.0.0), Biobase, multtest, survival Title: LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays Description: LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package. biocViews: Microarray, Statistics, DifferentialExpression, Preprocessing Author: David Rocke, Geun Cheol Lee, and John Tillinghast. Maintainer: John Tillinghast URL: http://www.idav.ucdavis.edu/~dmrocke/software.html License: LGPL source.ver: src/contrib/LMGene_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/LMGene_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/LMGene_1.6.0.tgz vignettes: vignettes/LMGene/inst/doc/LMGene.pdf Package: LPE Version: 1.10.0 Title: Methods for analyzing microarray data using Local Pooled Error (LPE) method Description: This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library. biocViews: Microarray, Statistics, DifferentialExpression Author: Nitin Jain , Michael O'Connell , Jae K. Lee . Includes R source code contributed by HyungJun Cho Maintainer: Nitin Jain URL: http://www.r-project.org, License: LGPL source.ver: src/contrib/LPE_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/LPE_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/LPE_1.10.0.tgz vignettes: vignettes/LPE/inst/doc/LPE.pdf Package: MANOR Version: 1.8.0 Depends: R(>= 1.8.0), GLAD Title: CGH Micro-Array NORmalization Description: We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. biocViews: Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, DNACopyNumber Author: Pierre Neuvial , Philippe Hupe Maintainer: Pierre Neuvial URL: http://bioinfo.curie.fr/projects/manor/index.html License: GPL source.ver: src/contrib/MANOR_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/MANOR_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/MANOR_1.8.0.tgz vignettes: vignettes/MANOR/inst/doc/MANOR.pdf Package: MLInterfaces Version: 1.10.3 Depends: R (>= 2.1), Biobase, methods, genefilter, rpart, rda Suggests: class, cluster, e1071, ipred, randomForest, gpls, pamr, rpart, MASS, nnet, ALL, gbm, mlbench, hgu95av2, som, RColorBrewer, hu6800, golubEsets, sma Title: Uniform interfaces to R machine learning procedures for data in Bioconductor containers Description: Uniform interfaces to machine learning code for data in Bioconductor containers biocViews: Statistics, Classification, Clustering Author: Jess Mar, Robert Gentleman, Vince Carey Maintainer: V. Carey License: LGPL source.ver: src/contrib/MLInterfaces_1.10.3.tar.gz win.binary.ver: bin/windows/contrib/2.5/MLInterfaces_1.10.3.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/MLInterfaces_1.10.3.tgz vignettes: vignettes/MLInterfaces/inst/doc/MLInterfaces.pdf, vignettes/MLInterfaces/inst/doc/xvalComputerClusters.pdf Package: MVCClass Version: 1.10.0 Depends: R (>= 2.1.0), methods Title: Model-View-Controller (MVC) Classes Description: Creates classes used in model-view-controller (MVC) design biocViews: Visualization, Infrastructure, GraphsAndNetworks Author: Elizabeth Whalen Maintainer: Elizabeth Whalen License: LGPL source.ver: src/contrib/MVCClass_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/MVCClass_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/MVCClass_1.10.0.tgz vignettes: vignettes/MVCClass/inst/doc/MVCClass.pdf Package: MantelCorr Version: 1.6.0 Depends: R (>= 2.0.0) Title: Compute Mantel Cluster Correlations Description: Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data). biocViews: Statistics, Clustering Author: Brian Steinmeyer and William Shannon Maintainer: Brian Steinmeyer License: GPL version 2 or newer? source.ver: src/contrib/MantelCorr_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/MantelCorr_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/MantelCorr_1.6.0.tgz vignettes: vignettes/MantelCorr/inst/doc/MantelCorrVignette.pdf Package: MassSpecWavelet Version: 1.2.0 Depends: waveslim Title: Mass spectrum processing by wavelet-based algorithms Description: Processing Mass Spectrometry spectrum by using wavelet based algorithm biocViews: MassSpectrometry, Proteomics Author: Pan Du, Warren Kibbe, Simon Lin Maintainer: Pan Du License: LGPL version 2 or newer source.ver: src/contrib/MassSpecWavelet_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/MassSpecWavelet_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/MassSpecWavelet_1.2.0.tgz vignettes: vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.pdf Package: MeasurementError.cor Version: 1.8.0 Title: Measurement Error model estimate for correlation coefficient Description: Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation biocViews: Statistics Author: Beiying Ding Maintainer: Beiying Ding License: LGPL source.ver: src/contrib/MeasurementError.cor_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/MeasurementError.cor_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/MeasurementError.cor_1.8.0.tgz vignettes: vignettes/MeasurementError.cor/inst/doc/MeasurementError.cor.pdf Package: MergeMaid Version: 2.8.0 Depends: R (>= 2.2.0), survival, Biobase, MASS, methods Title: Merge Maid Description: The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix','exprSet' or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival. biocViews: Microarray, DifferentialExpression, Visualization Author: Xiaogang Zhong Leslie Cope Elizabeth Garrett Giovanni Parmigiani Maintainer: Xiaogang Zhong URL: http://astor.som.jhmi.edu/MergeMaid License: GPL version 2 or higher source.ver: src/contrib/MergeMaid_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/MergeMaid_2.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/MergeMaid_2.8.0.tgz vignettes: vignettes/MergeMaid/inst/doc/MergeMaid.pdf Package: Mfuzz Version: 1.6.0 Depends: R (>= 2.5.0), Biobase, e1071 Suggests: marray Title: Soft clustering of time series gene expression data Description: Package for noise-robust soft clustering of gene expression data biocViews: Microarray, Clustering, TimeCourse Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/index.html License: GPL version 2 source.ver: src/contrib/Mfuzz_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/Mfuzz_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Mfuzz_1.6.0.tgz vignettes: vignettes/Mfuzz/inst/doc/Mfuzz.pdf Package: MiPP Version: 1.8.0 Depends: R (>= 2.4), Biobase, e1071,MASS Title: Misclassification Penalized Posterior Classification Description: This package finds optimal sets of genes that seperate samples into two or more classes. biocViews: Microarray, Classification Author: HyungJun Cho , Sukwoo Kim , Mat Soukup , and Jae K. Lee Maintainer: Sukwoo Kim URL: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ License: GPL version 2 or newer source.ver: src/contrib/MiPP_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/MiPP_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/MiPP_1.8.0.tgz vignettes: vignettes/MiPP/inst/doc/MiPP.pdf Package: OCplus Version: 1.10.0 Depends: R (>= 2.1.0), akima, multtest (>= 1.7.3) Title: Operating characteristics plus sample size and local fdr for microarray experiments Description: This package allows to characterize the operating characeristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). biocViews: Microarray, Statistics, DifferentialExpression, MultipleComparisons Author: Yudi Pawitan and Alexander Ploner Maintainer: Alexander Ploner License: LGPL source.ver: src/contrib/OCplus_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/OCplus_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/OCplus_1.10.0.tgz vignettes: vignettes/OCplus/inst/doc/OCplus.pdf Package: OLIN Version: 1.12.0 Depends: R (>= 2.5.0), methods, stats, locfit, Biobase, marray Suggests: convert, limma Title: Optimized local intensity-dependent normalisation of two-color microarrays Description: Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data biocViews: Microarray, TwoChannel, QualityControl, Preprocessing, Visualization Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN License: GPL version 2 source.ver: src/contrib/OLIN_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/OLIN_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/OLIN_1.12.0.tgz vignettes: vignettes/OLIN/inst/doc/OLIN.pdf Package: OLINgui Version: 1.10.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Suggests: tcltk, tkWidgets Title: Graphical user interface for OLIN Description: Graphical user interface for the OLIN package biocViews: Microarray, TwoChannel, QualityControl, Preprocessing, Visualization Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN License: GPL version 2 source.ver: src/contrib/OLINgui_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/OLINgui_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/OLINgui_1.10.0.tgz vignettes: vignettes/OLINgui/inst/doc/OLINgui.pdf, vignettes/OLINgui/inst/doc/OLINguiScreenshot.pdf Package: OrderedList Version: 1.8.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2) Title: Similarities of Ordered Gene Lists Description: Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. biocViews: Microarray, DifferentialExpression, MultipleComparisons Author: Xinan Yang, Stefanie Scheid, Claudio Lottaz Maintainer: Claudio Lottaz URL: http://compdiag.molgen.mpg.de/software/index.shtml License: GPL version 2.0 or newer source.ver: src/contrib/OrderedList_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/OrderedList_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/OrderedList_1.8.0.tgz vignettes: vignettes/OrderedList/inst/doc/bcb_logo.pdf, vignettes/OrderedList/inst/doc/tr_2006_01.pdf Package: PGSEA Version: 1.2.0 Depends: methods, Biobase, Ruuid Suggests: GO Title: Parametric Gene Set Enrichment Analysis Description: Parametric Analysis of Gene Set Enrichment biocViews: Microarray Author: Kyle Furge and Karl Dykema Maintainer: Karl Dykema License: GPL2 source.ver: src/contrib/PGSEA_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/PGSEA_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/PGSEA_1.2.0.tgz vignettes: vignettes/PGSEA/inst/doc/PGSEA.pdf Package: PROcess Version: 1.12.0 Depends: Icens Title: Ciphergen SELDI-TOF Processing Description: A package for processing protein mass spectrometry data. biocViews: MassSpectrometry, Proteomics Author: Xiaochun Li Maintainer: Xiaochun Li License: Artistic source.ver: src/contrib/PROcess_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/PROcess_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/PROcess_1.12.0.tgz vignettes: vignettes/PROcess/inst/doc/howtoprocess.pdf Package: RBGL Version: 1.12.0 Depends: graph, methods Imports: methods Title: Interface to boost C++ graph lib Description: demo of interface with full copy of all hpp defining boost biocViews: GraphsAndNetworks Author: Vince Carey , Li Long , R. Gentleman Maintainer: Li Long URL: http://www.bioconductor.org License: The Artistic License, Version 2.0 source.ver: src/contrib/RBGL_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/RBGL_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/RBGL_1.12.0.tgz vignettes: vignettes/RBGL/inst/doc/RBGL.pdf, vignettes/RBGL/inst/doc/filedep.pdf Package: RMAGEML Version: 2.10.0 Depends: methods, marray, limma, Biobase Title: Handling MAGEML documents Description: This package can be used to handle MAGEML documents in Bioconductor biocViews: Microarray Author: Steffen Durinck , Joke Allemeersch and Vincent Carey Maintainer: Steffen Durinck URL: http://www.esat.kuleuven.ac.be/~jallemee,http://www.esat.kuleuven.ac.be/~sdurinck License: LGPL version source.ver: src/contrib/RMAGEML_2.10.0.tar.gz vignettes: vignettes/RMAGEML/inst/doc/RMAGEML.pdf Package: RMAPPER Version: 1.6.0 Depends: methods Suggests: RCurl Title: interface to mapper.chip.org Description: employs http interface to mapper TFBS database biocViews: Annotation, Genetics Author: VJ Carey Maintainer: VJ Carey License: LGPL source.ver: src/contrib/RMAPPER_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/RMAPPER_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/RMAPPER_1.6.0.tgz Package: ROC Version: 1.10.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase Title: utilities for ROC, with uarray focus Description: utilities for ROC, with uarray focus biocViews: Statistics, DifferentialExpression Author: Vince Carey , Henning Redestig for C++ language enhancements Maintainer: Vince Carey URL: http://www.bioconductor.org License: LGPL source.ver: src/contrib/ROC_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/ROC_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ROC_1.10.0.tgz vignettes: vignettes/ROC/inst/doc/ROCnotes.pdf Package: RSNPper Version: 1.10.0 Depends: methods, utils, tools, XML Title: interface to chip.org::SNPper for SNP-related data Description: bindings to the XML RPC services of chip.org::SNPper biocViews: Annotation, Genetics, SNPsAndGeneticVariability Author: VJ Carey Maintainer: VJ Carey License: GPL source.ver: src/contrib/RSNPper_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/RSNPper_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/RSNPper_1.10.0.tgz vignettes: vignettes/RSNPper/inst/doc/RSNPper.pdf Package: RWebServices Version: 1.0.0 Depends: SJava (>= 0.69-4), TypeInfo, methods, tools, R (>= 2.5.0) Title: Expose R functions as web services through Java/Axis/Apache Description: This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment. biocViews: Infrastructure Author: Nianhua Li, MT Morgan Maintainer: Biocore Team License: caBIG source.ver: src/contrib/RWebServices_1.0.0.tar.gz vignettes: vignettes/RWebServices/inst/doc/EnablingPackages.pdf, vignettes/RWebServices/inst/doc/InstallingAndTesting.pdf, vignettes/RWebServices/inst/doc/LessonsLearned.pdf, vignettes/RWebServices/inst/doc/RToJava.pdf, vignettes/RWebServices/inst/doc/RelatedWork.pdf, vignettes/RWebServices/inst/doc/rtypes.pdf Package: RankProd Version: 2.8.0 Depends: R (>= 1.9.0) Title: Rank Product method for identifying differentially expressed genes with application in meta-analysis Description: Non-paramteric method for identifying differentially expressed (up- or down- regulated )genes based on the estimated percentage of false predictions (pfp).The method can combine data sets from different origins (meta-analysis)to increase the power of the identification. biocViews: DifferentialExpression Author: Fangxin Hong and Ben Wittner with contribution from Rainer Breitling and Colin Smith Maintainer: Fangxin Hong License: free for non-commercial users. Non-academic users MUST have requested from the author source.ver: src/contrib/RankProd_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/RankProd_2.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/RankProd_2.8.0.tgz vignettes: vignettes/RankProd/inst/doc/RankProd.pdf Package: RbcBook1 Version: 1.4.0 Depends: Biobase, graph Title: Support for Springer monograph on Bioconductor Description: tools for building book Author: Vince Carey and Wolfgang Huber Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey License: The Artistic License, Version 2.0 source.ver: src/contrib/RbcBook1_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/RbcBook1_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/RbcBook1_1.4.0.tgz vignettes: vignettes/RbcBook1/inst/doc/RbcBook1.pdf Package: RdbiPgSQL Version: 1.10.0 Depends: R (>= 1.2), Rdbi Title: PostgreSQL access Description: Provides methods for accessing data stored in PostgreSQL tables. Code written by Timothy H. Keitt and modified by Jianhua Zhang biocViews: Infrastructure Author: Timothy H. Keitt Maintainer: Jianhua Zhang License: GPL source.ver: src/contrib/RdbiPgSQL_1.10.0.tar.gz Package: Rdbi Version: 1.10.0 Depends: R (>= 1.2) Title: Generic database methods Description: Generic framework for database access in R. Code written by Timothy H. Keitt and modified by Jianhua Zhang biocViews: Infrastructure Author: Timothy H. Keitt Maintainer: Jianhua Zhang License: GPL source.ver: src/contrib/Rdbi_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/Rdbi_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Rdbi_1.10.0.tgz Package: RefPlus Version: 1.4.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), affy (>= 1.6.7), affyPLM (>= 1.3.3) Title: A function set for the RMA+ and the RMA++ methods. Description: The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods. biocViews: Microarray, OneChannel, Preprocessing Author: Kai-Ming Chang Maintainer: Kai-Ming Chang License: GPL version 2 or newer source.ver: src/contrib/RefPlus_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/RefPlus_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/RefPlus_1.4.0.tgz vignettes: vignettes/RefPlus/inst/doc/RefPlus.pdf Package: Resourcerer Version: 1.10.0 Depends: R (>= 1.9.0), Biobase, AnnBuilder (>= 1.5.31) Title: Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. Description: This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. biocViews: Annotation, Microarray Author: Jianhua Zhang Maintainer: Jianhua Zhang License: LGPL source.ver: src/contrib/Resourcerer_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/Resourcerer_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Resourcerer_1.10.0.tgz vignettes: vignettes/Resourcerer/inst/doc/Resourcerer.pdf Package: Rgraphviz Version: 1.14.1 Depends: R (>= 2.4.0), methods, utils, graph, geneplotter (>= 1.11.3) Imports: utils Suggests: Biobase, fibroEset, hgu95av2 Title: Provides plotting capabilities for R graph objects Description: Interfaces R with the AT&T GraphViz library to provide the ability for plotting R graph objects from the graph package biocViews: GraphsAndNetworks Author: Jeff Gentry , Li Long , Robert Gentleman , Seth Falcon Maintainer: Li Long License: The Artistic License, Version 2.0 SystemRequirements: Graphviz version >= 2.2 source.ver: src/contrib/Rgraphviz_1.14.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/Rgraphviz_1.14.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Rgraphviz_1.14.1.tgz vignettes: vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf, vignettes/Rgraphviz/inst/doc/layingOutPathways.pdf Package: Ringo Version: 1.0.0 Depends: graphics, methods, Biobase, geneplotter, limma, vsn, RColorBrewer Title: R Investigation of NimbleGen Oligoarrays Description: The package Ringo simplifies the analysis of two-color oligonucleotide microarrays from NimbleGen, which for example can be used in ChIP-chip projects. The package employs functions from various other packages of the Bioconductor project and provides additional NimbleGen-specific and ChIP-chip-specific functionalities. Its mainly covered subjects are data read-in, quality control, visualisation and identification of genomic regions showing enrichment in ChIP-chip. Please take note that Ringo is geared towards two-color NimbleGen microarrays. For single-channel NimbleGen arrays, we recommend the package 'oligo'. biocViews: Microarray,TwoChannel,DataImport,QualityControl,Preprocessing Author: Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie Maintainer: J. Toedling License: Artistic License 2.0 source.ver: src/contrib/Ringo_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/Ringo_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Ringo_1.0.0.tgz vignettes: vignettes/Ringo/inst/doc/Ringo.pdf Package: Rredland Version: 1.4.0 Depends: methods, graph Title: interface to redland RDF utilities Description: interface to redland RDF utilities; assumes librdf, possibly berkeley DB; include OWL files from www.biopax.org, and RDF serializations of various resources from ISB-SIB.CH; redland is a production of Dave Beckett (see librdf.org) biocViews: Infrastructure Author: VJ Carey Maintainer: VJ Carey URL: http://www.bioconductor.org License: LGPL version 2.1 source.ver: src/contrib/Rredland_1.4.0.tar.gz vignettes: vignettes/Rredland/inst/doc/Rredland.pdf Package: Ruuid Version: 1.14.0 Depends: R (>= 2.1), methods Imports: methods Title: Ruuid: Provides Universally Unique ID values Description: A package to provide UUID values in R biocViews: Infrastructure, Technology Author: R. Gentleman Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/Ruuid_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/Ruuid_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/Ruuid_1.14.0.tgz vignettes: vignettes/Ruuid/inst/doc/Ruuid.pdf Package: SAGElyzer Version: 1.14.0 Depends: R (>= 1.6.0),AnnBuilder,tkWidgets,genefilter,annotate,Biobase Title: A package that deals with SAGE libraries Description: This package provides functions to puts SAGE library data into a datbase, calls genefinder to find genes that are similar to a given SAGE tag biocViews: Technology, SAGE Author: Jianhua Zhang Maintainer: Jianhua Zhang License: LGPL source.ver: src/contrib/SAGElyzer_1.14.0.tar.gz vignettes: vignettes/SAGElyzer/inst/doc/SAGElyzer.pdf Package: SAGx Version: 1.10.1 Depends: R (>= 2.3.1), stats, multtest, methods Imports: Biobase Suggests: KEGG, hu6800 Title: Statistical Analysis of the GeneChip Description: A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed. biocViews: Microarray, OneChannel, Preprocessing, DataImport, Statistics, DifferentialExpression, Clustering, MultipleComparisons Author: Per Broberg Maintainer: Per Broberg URL: http://home.swipnet.se/pibroberg/expression_hemsida1.html License: GNU GPL. source.ver: src/contrib/SAGx_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/SAGx_1.10.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/SAGx_1.10.1.tgz vignettes: vignettes/SAGx/inst/doc/samroc-ex.pdf Package: SBMLR Version: 1.30.0 Depends: XML,odesolve Title: SBML-R Interface and Analysis Tools Description: This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples. biocViews: GraphsAndNetworks Author: Tomas Radivoyevitch Maintainer: Tomas Radivoyevitch URL: http://epbi-radivot.cwru.edu/ License: GPL source.ver: src/contrib/SBMLR_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/SBMLR_1.30.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/SBMLR_1.30.0.tgz vignettes: vignettes/SBMLR/inst/doc/BMC.BioInformatics04.pdf, vignettes/SBMLR/inst/doc/manual.pdf Package: SLqPCR Version: 1.2.0 Depends: R(>= 2.4.0), stats, RColorBrewer Title: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH Description: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH biocViews: Statistics Author: Matthias Kohl Maintainer: Matthias Kohl License: GPL (version 2 or later) source.ver: src/contrib/SLqPCR_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/SLqPCR_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/SLqPCR_1.2.0.tgz vignettes: vignettes/SLqPCR/inst/doc/SLqPCR-fig2.pdf, vignettes/SLqPCR/inst/doc/SLqPCR-fig3a.pdf, vignettes/SLqPCR/inst/doc/SLqPCR.pdf Package: SNPchip Version: 1.0.0 Depends: R (>= 2.5.0), Biobase (>= 1.11.0), tools, methods, geneplotter, oligo, stats, graphics Title: Classes and Methods for high throughput SNP chip data Description: A collection of tools for high throughput SNP chip data. biocViews: DNACopyNumber, SNPsAndGeneticVariability, Visualization Author: Robert Scharpf , Jason Ting, Jonathon Pevsner, and Ingo Ruczinski Maintainer: Robert Scharpf URL: http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html License: GPL version 2 or newer source.ver: src/contrib/SNPchip_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/SNPchip_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/SNPchip_1.0.0.tgz vignettes: vignettes/SNPchip/inst/doc/SNPchip.pdf Package: ScISI Version: 1.8.0 Depends: methods, apComplex, GO, GOstats, graph, RBGL, Rgraphviz, YEAST, xtable, Matrix Suggests: ppiData, ppiStats Title: In Silico Interactome Description: Package to create In Silico Interactomes biocViews: GraphsAndNetworks, Proteomics Author: Tony Chiang Maintainer: Tony Chiang License: LGPL source.ver: src/contrib/ScISI_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/ScISI_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ScISI_1.8.0.tgz vignettes: vignettes/ScISI/inst/doc/ScISI.pdf, vignettes/ScISI/inst/doc/ScISIsupp.pdf, vignettes/ScISI/inst/doc/vignette.pdf Package: SemSim Version: 1.2.0 Depends: GO, annotate Suggests: cluster, hgu133plus2 Title: Gene Ontology-based Semantic Similarity Measures Description: Implementation of semantic similarity measures based on information content of Gene Ontology terms. biocViews: GO Author: Xiang Guo Maintainer: Xiang Guo License: GPL version 2 source.ver: src/contrib/SemSim_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/SemSim_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/SemSim_1.2.0.tgz vignettes: vignettes/SemSim/inst/doc/SemSim.pdf Package: TypeInfo Version: 1.2.0 Depends: methods Title: Optional Type Specification Prototype Description: A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions. Additionally, the arguments in a call to a typed function can be validated using the type specifications. We allow types to be specified as either i) by class name using either inheritance - is(x, className), or strict instance of - class(x) %in% className, or ii) a dynamic test given as an R expression which is evaluated at run-time. More precise information and interesting tests can be done via ii), but it is harder to use this information as meta-data as it requires more effort to interpret it and it is of course run-time information. It is typically more meaningful. biocViews: Infrastructure Author: Duncan Temple Lang Robert Gentleman () Maintainer: Duncan Temple Lang License: BSD source.ver: src/contrib/TypeInfo_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/TypeInfo_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/TypeInfo_1.2.0.tgz vignettes: vignettes/TypeInfo/inst/doc/TypeInfoNews.pdf Package: aCGH Version: 1.10.0 Depends: R (>= 1.8.0), cluster, survival, multtest, sma Title: Classes and functions for Array Comparative Genomic Hybridization data. Description: Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. biocViews: DNACopyNumber, DataImport, Genetics Author: Jane Fridlyand , Peter Dimitrov Maintainer: Jane Fridlyand License: GPL source.ver: src/contrib/aCGH_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/aCGH_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/aCGH_1.10.0.tgz vignettes: vignettes/aCGH/inst/doc/aCGH.pdf Package: adSplit Version: 1.6.0 Depends: R (>= 2.1.0), methods (>= 2.1.0), stats (>= 2.1.0), cluster (>= 1.9.1), multtest (>= 1.6.0), Biobase (>= 1.5.12), affy (>= 1.6.7), GO (>= 1.8.1), KEGG (>= 1.8.1) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800 (>= 1.8.1) Title: Annotation-Driven Clustering Description: This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined. biocViews: Microarray, Statistics, Clustering Author: Claudio Lottaz, Joern Toedling Maintainer: Claudio Lottaz URL: http://compdiag.molgen.mpg.de/software/index.shtml License: GPL version 2.0 or newer source.ver: src/contrib/adSplit_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/adSplit_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/adSplit_1.6.0.tgz vignettes: vignettes/adSplit/inst/doc/bcb_logo.pdf, vignettes/adSplit/inst/doc/minerva_bcb.pdf, vignettes/adSplit/inst/doc/tr_2005_02.pdf Package: affxparser Version: 1.8.3 Depends: R (>= 2.5.0) Suggests: R.utils Title: Affymetrix File Parsing SDK Description: Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure. biocViews: DataImport Author: Henrik Bengtsson, James Bullard, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen License: LGPL-2 source.ver: src/contrib/affxparser_1.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.5/affxparser_1.8.3.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affxparser_1.8.3.tgz Package: affyPLM Version: 1.12.0 Depends: R (>= 2.4.0), affy (>= 1.11.0), affydata, Biobase, methods, gcrma, stats Title: Methods for fitting probe-level models 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. biocViews: Microarray, OneChannel, Preprocessing, QualityControl Author: Ben Bolstad Maintainer: Ben Bolstad URL: http://bmbolstad.com License: GPL version 2 or newer source.ver: src/contrib/affyPLM_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/affyPLM_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affyPLM_1.12.0.tgz vignettes: vignettes/affyPLM/inst/doc/AffyExtensions.pdf, vignettes/affyPLM/inst/doc/MAplots.pdf, vignettes/affyPLM/inst/doc/QualityAssess.pdf, vignettes/affyPLM/inst/doc/ThreeStep.pdf Package: affyQCReport Version: 1.14.0 Depends: Biobase (>= 1.13.16), affy, simpleaffy, xtable, affyPLM, RColorBrewer, geneplotter, lattice Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1) Title: QC Report Generation for affyBatch objects Description: This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. biocViews: Microarray,OneChannel,QualityControl Author: Craig Parman , Conrad Halling , Robert Gentleman Maintainer: Craig Parman License: LGPL version 2 or newer source.ver: src/contrib/affyQCReport_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/affyQCReport_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affyQCReport_1.14.0.tgz vignettes: vignettes/affyQCReport/inst/doc/affyQCReport.pdf Package: affy Version: 1.14.2 Depends: R (>= 2.4.0), Biobase (>= 1.13.41), methods, utils, affyio (>= 1.4.0) Suggests: tkWidgets (>= 1.2.2), affydata, geneplotter Title: Methods for Affymetrix Oligonucleotide Arrays Description: The package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it. biocViews: Microarray, OneChannel, Preprocessing Author: Rafael A. Irizarry , Laurent Gautier , Benjamin Milo Bolstad , and Crispin Miller with contributions from Magnus Astrand , Leslie M. Cope , Robert Gentleman, Jeff Gentry, Conrad Halling , Wolfgang Huber, James MacDonald , Benjamin I. P. Rubinstein, Christopher Workman , John Zhang Maintainer: Rafael A. Irizarry License: LGPL version 2 or newer source.ver: src/contrib/affy_1.14.2.tar.gz win.binary.ver: bin/windows/contrib/2.5/affy_1.14.2.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affy_1.14.2.tgz vignettes: vignettes/affy/inst/doc/affy.pdf, vignettes/affy/inst/doc/builtinMethods.pdf, vignettes/affy/inst/doc/customMethods.pdf, vignettes/affy/inst/doc/dealing_with_cdfenvs.pdf, vignettes/affy/inst/doc/vim.pdf Package: affycomp Version: 1.12.0 Depends: R (>= 2.4.0), methods, Biobase (>= 1.13.57) Title: Graphics Toolbox for Assessment of Affymetrix Expression Measures Description: The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. biocViews: OneChannel, Microarray, Preprocessing Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley , Maintainer: Rafael A. Irizarry License: GPL version 2 or newer source.ver: src/contrib/affycomp_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/affycomp_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affycomp_1.12.0.tgz vignettes: vignettes/affycomp/inst/doc/affycomp.pdf Package: affycoretools Version: 1.8.1 Depends: affy, limma, GOstats, biomaRt, gcrma, Biobase, annotate, xtable, annaffy Suggests: hgfocus, hgfocuscdf Title: Functions useful for those doing repetitive analyses with Affymetrix GeneChips. Description: Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see. biocViews: ReportWriting, Microarray, OneChannel, Preprocessing Author: James W. MacDonald Maintainer: James W. MacDonald License: Artistic source.ver: src/contrib/affycoretools_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/affycoretools_1.8.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affycoretools_1.8.1.tgz vignettes: vignettes/affycoretools/inst/doc/affycoretools.pdf, vignettes/affycoretools/inst/doc/affycoretools_biomaRt.pdf Package: affyio Version: 1.4.1 Depends: methods Title: Tools for parsing Affymetrix data files Description: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats. biocViews: Microarray, DataImport Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad License: LGPL version 2 or newer source.ver: src/contrib/affyio_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/affyio_1.4.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affyio_1.4.1.tgz Package: affylmGUI Version: 1.10.4 Depends: limma, tcltk, affy, Biobase, affyio Suggests: tkrplot, affyPLM, R2HTML, xtable Title: GUI for affy analysis using limma package Description: A Graphical User Interface for affy analysis using the limma Microarray package biocViews: Microarray, OneChannel, DataImport, QualityControl, Preprocessing, Statistics, DifferentialExpression, MultipleComparisons Author: James Wettenhall and Ken Simpson Division of Genetics and Bioinformatics, WEHI. Maintainer: Keith Satterley URL: http://bioinf.wehi.edu.au/affylmGUI/ License: GPL version 2 or newer source.ver: src/contrib/affylmGUI_1.10.4.tar.gz win.binary.ver: bin/windows/contrib/2.5/affylmGUI_1.10.4.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affylmGUI_1.10.4.tgz vignettes: vignettes/affylmGUI/inst/doc/affylmGUI.pdf, vignettes/affylmGUI/inst/doc/extract.pdf Package: affypdnn Version: 1.10.0 Depends: R (>= 2.3.0), affy (>= 1.5), affydata, hgu95av2probe Title: Probe Dependent Nearest Neighbours (PDNN) for the affy package Description: The package contains functions to perform the PDNN method described by Li Zhang et al. biocViews: OneChannel, Microarray, Preprocessing Author: H. Bjorn Nielsen and Laurent Gautier (Many thanks to Li Zhang early communications about the existence of the PDNN program and related publications). Maintainer: Laurent Gautier License: LGPL source.ver: src/contrib/affypdnn_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/affypdnn_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/affypdnn_1.10.0.tgz Package: altcdfenvs Version: 1.10.0 Depends: R (>= 2.5), methods, Biobase, affy, matchprobes, makecdfenv Suggests: splicegear, plasmodiumanophelescdf, hgu95acdf, hgu133aprobe Title: alternative cdfenvs Description: Convenience data structures and functions to handle cdfenvs biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Annotation, ProprietaryPlatforms, Transcription Author: Laurent Gautier Maintainer: Laurent Gautier License: GPL version 2 or newer source.ver: src/contrib/altcdfenvs_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/altcdfenvs_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/altcdfenvs_1.10.0.tgz vignettes: vignettes/altcdfenvs/inst/doc/altcdfenvs.pdf, vignettes/altcdfenvs/inst/doc/modify.pdf, vignettes/altcdfenvs/inst/doc/ngenomeschips.pdf Package: annaffy Version: 1.8.1 Depends: R (>= 2.4.0), methods, Biobase, GO (>= 1.6.0), KEGG Suggests: hgu95av2, multtest, tcltk Title: Annotation tools for Affymetrix biological metadata Description: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. biocViews: OneChannel, Microarray, Annotation, GO, Pathways, ReportWriting Author: Colin A. Smith Maintainer: Colin A. Smith License: LGPL source.ver: src/contrib/annaffy_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/annaffy_1.8.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/annaffy_1.8.1.tgz vignettes: vignettes/annaffy/inst/doc/annaffy.pdf Package: annotate Version: 1.14.1 Depends: R (>= 2.4.0), methods, Biobase Suggests: hgu95av2, genefilter, Biostrings (>= 2.1.2), rae230a, rae230aprobe, tkWidgets, XML (>= 0.92-2), hsahomology, xlahomology, GO Title: Annotation for microarrays Description: Using R enviroments for annotation. biocViews: Annotation, Pathways, GO, Affymetrix Author: R. Gentleman Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/annotate_1.14.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/annotate_1.14.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/annotate_1.14.1.tgz vignettes: vignettes/annotate/inst/doc/GOusage.pdf, vignettes/annotate/inst/doc/annotate.pdf, vignettes/annotate/inst/doc/chromLoc.pdf, vignettes/annotate/inst/doc/prettyOutput.pdf, vignettes/annotate/inst/doc/query.pdf, vignettes/annotate/inst/doc/useDataPkgs.pdf, vignettes/annotate/inst/doc/useHomology.pdf, vignettes/annotate/inst/doc/useProbeInfo.pdf Package: annotationTools Version: 1.4.0 Depends: Biobase Title: Annotate microarrays and find orthologs using flat file databases Description: Functions to annotate microarrays and mine for orthologs from flat file databases (plain text files). biocViews: Microarray, Annotation Author: Alexandre Kuhn Maintainer: Alexandre Kuhn License: GPL source.ver: src/contrib/annotationTools_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/annotationTools_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/annotationTools_1.4.0.tgz vignettes: vignettes/annotationTools/inst/doc/annotationTools.pdf Package: apComplex Version: 2.2.0 Depends: graph, RBGL Suggests: Rgraphviz Title: Estimate protein complex membership using AP-MS protein data Description: Functions to estimate a bipartite graph of protein complex membership using AP-MS data. biocViews: Visualization, MassSpectrometry, GraphsAndNetworks Author: Denise Scholtens Maintainer: Denise Scholtens License: LGPL source.ver: src/contrib/apComplex_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/apComplex_2.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/apComplex_2.2.0.tgz vignettes: vignettes/apComplex/inst/doc/apComplex.pdf Package: aroma.light Version: 1.4.0 Depends: R.oo Suggests: R.utils Title: Light-weight methods for normalization and visualization of microarray data using only basic R data types Description: Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. biocViews: Microarray, OneChannel, TwoChannel, Preprocessing Author: Henrik Bengtsson Maintainer: Henrik Bengtsson URL: http://www.braju.com/R/ License: LGPL source.ver: src/contrib/aroma.light_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/aroma.light_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/aroma.light_1.4.0.tgz Package: arrayMagic Version: 1.14.0 Depends: R (>= 2.1.0), methods, utils, Biobase, vsn (>= 1.4.10), limma (>= 1.7.6), genefilter (>= 1.5.2) Title: two-colour cDNA array quality control and preprocessing Description: A collection of utilities for quality control and processing of two-colour cDNA microarray data biocViews: Microarray,TwoChannel,DataImport,QualityControl,Preprocessing Author: Andreas Buness and Wolfgang Huber Maintainer: Andreas Buness URL: http://www.dkfz-heidelberg.de/abt0840/home/buness/WWW/Software/arrayMagic/ License: BSD; read file BSD.license source.ver: src/contrib/arrayMagic_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/arrayMagic_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/arrayMagic_1.14.0.tgz vignettes: vignettes/arrayMagic/inst/doc/arrayMagicVignette.pdf Package: arrayQCplot Version: 2.4.0 Depends: RGtk2, cairoDevice, LPE Title: Explore microarray data and check quality and reproducibility. Description: Check reliabilility and reproducibility biocViews: Microarray,QualityControl, Visualization Author: Eun-kyung Lee, Sung-Gon Yi,Taesung Park Maintainer: Eun-kyung Lee License: BSD See file LICENCE. source.ver: src/contrib/arrayQCplot_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/arrayQCplot_2.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/arrayQCplot_2.4.0.tgz vignettes: vignettes/arrayQCplot/inst/doc/arrayQCplot-manual.pdf Package: arrayQuality Version: 1.12.0 Depends: R (>= 2.2.0), marray, limma, convert, hexbin, gridBase, RColorBrewer Suggests: mclust, MEEBOdata, HEEBOdata Title: Assessing array quality on spotted arrays Description: Functions for performing print-run and array level quality assessment. biocViews: Microarray,TwoChannel,QualityControl,Visualization Author: Agnes Paquet and Jean Yee Hwa Yang Maintainer: Agnes Paquet URL: http://arrays.ucsf.edu/ License: LGPL source.ver: src/contrib/arrayQuality_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/arrayQuality_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/arrayQuality_1.12.0.tgz Package: beadarraySNP Version: 1.2.0 Depends: methods, tools, Biobase, quantsmooth Suggests: aCGH, affy, limma, snapCGH Title: Normalization and reporting of Illumina SNP bead arrays Description: Importing data from Illumina SNP experiments and performing copy number calculations and reports. biocViews: DNACopyNumber, SNPsAndGeneticVariability, TwoChannel, Preprocessing, DataImport Author: Jan Oosting Maintainer: Jan Oosting License: GPL V2 source.ver: src/contrib/beadarraySNP_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/beadarraySNP_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/beadarraySNP_1.2.0.tgz vignettes: vignettes/beadarraySNP/inst/doc/beadarraySNP.pdf Package: beadarray Version: 1.4.0 Depends: limma, Biobase, geneplotter, methods, affy, beadarraySNP Suggests: vsn Title: Quality control and low-level analysis of BeadArrays Description: The package is able to read pre-processed Bead Summary data as well as re-constructing bead-level data using raw TIFF images. Methods for quality control and low-level analysis are provided. biocViews: Microarray, OneChannel, QualityControl, Preprocessing Author: Mark Dunning, Mike Smith, Isabelle Camilier, Matt Ritchie Maintainer: Mark Dunning License: GPL source.ver: src/contrib/beadarray_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/beadarray_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/beadarray_1.4.0.tgz vignettes: vignettes/beadarray/inst/doc/Analysis-of-Bead-Summary-data-using-beadarray.pdf, vignettes/beadarray/inst/doc/Analysis-of-bead-level-data-using-beadarray.pdf Package: bgx Version: 1.0.21 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Suggests: affydata, hgu95av2cdf Title: Bayesian Gene eXpression Description: Bayesian integrated analysis of Affymetrix GeneChips biocViews: Microarray, DifferentialExpression Author: Ernest Turro, Graeme Ambler, Anne-Mette K Hein Maintainer: Ernest Turro License: GPL source.ver: src/contrib/bgx_1.0.21.tar.gz win.binary.ver: bin/windows/contrib/2.5/bgx_1.0.21.zip vignettes: vignettes/bgx/inst/doc/bgx.pdf Package: bioDist Version: 1.8.0 Depends: R (>= 2.0), methods, Biobase Suggests: locfit Title: Different distance measures Description: A collection of software tools for calculating distance measures. biocViews: Statistics Author: B. Ding, R. Gentleman and Vincent Carey Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/bioDist_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/bioDist_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/bioDist_1.8.0.tgz Package: biocViews Version: 1.4.0 Depends: R (>= 2.4.0), methods, tools, graph (>= 1.9.26), RBGL, XML Title: Categorized views of R package repositories Description: structures for vocabularies and narratives of views biocViews: Infrastructure Author: VJ Carey , BJ Harshfield , S Falcon Maintainer: Seth Falcon URL: http://bioconductor.org/packages/1.8/TaskViews.html License: LGPL version source.ver: src/contrib/biocViews_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/biocViews_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/biocViews_1.4.0.tgz vignettes: vignettes/biocViews/inst/doc/HOWTO-BCV.pdf, vignettes/biocViews/inst/doc/createReposHtml.pdf Package: biomaRt Version: 1.10.1 Depends: methods, XML, RCurl Suggests: annotate Title: Interface to BioMart databases (e.g. Ensembl, Wormbase, Gramene and Uniprot) Description: The package provides an API in R to query BioMart databases such as Ensembl (http://www.ensembl.org), a software system which produces and maintains automatic annotation on metazoan genomes. Two sets of functions are currently implemented. A first set of functions aims to mimic functionality of other BioMart APIs such as Martshell, Martview, etc. (see http://www.biomart.org for more information). These functions are very general, and can be used with any BioMart system. They allow retrieval of all information that other BioMart APIs provide and enable data mining of the respective databases. A Second set of functions are tailored towards Ensembl and are a set of commonly used queries in microarray data analysis. With these two sets of functions, one can for example annotate the features on your array with the latest annotations starting from identifiers such as Affymetrix, RefSeq, entrezgene,.. Annotation includes gene names, GO, OMIM annotation, etc. The package also provides homology mappings between these identifiers across all species present in Ensembl. Genes can be pre-selected such that they fulfill a certain requirement e.g. give all human RefSeq ids of genes known to be involved in diabetes. On top of this, biomaRt enables you to retrieve any type of information available from the BioMart databases from R. Other examples of BioMart databases are Wormbase and Gramene. biocViews: Annotation Author: Steffen Durinck , Wolfgang Huber , Sean Davis Maintainer: Steffen Durinck License: Artistic License 2.0 source.ver: src/contrib/biomaRt_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/biomaRt_1.10.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/biomaRt_1.10.1.tgz vignettes: vignettes/biomaRt/inst/doc/biomaRt.pdf, vignettes/biomaRt/inst/doc/prettyOutput.pdf Package: bridge Version: 1.8.0 Depends: R (>= 1.9.0), rama Title: Bayesian Robust Inference for Differential Gene Expression Description: Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. biocViews: Microarray,OneChannel,TwoChannel,DifferentialExpression Author: Raphael Gottardo Maintainer: Raphael Gottardo License: GPL version 2 or newer source.ver: src/contrib/bridge_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/bridge_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/bridge_1.8.0.tgz vignettes: vignettes/bridge/inst/doc/bridge.pdf Package: cellHTS Version: 1.6.0 Depends: R (>= 2.5.0), prada (>= 1.9.4), RColorBrewer, Biobase (>= 1.11.12), genefilter (>= 1.11.2) Suggests: Category, GO, vsn (>= 2.0.35) Title: Analysis of cell-based screens Description: Analysis of cell-based RNA interference screens biocViews: CellBasedAssays, Preprocessing, Visualization Author: Wolfgang Huber , Ligia Bras , Michael Boutros Maintainer: Ligia Bras URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber License: Artistic License 2.0 source.ver: src/contrib/cellHTS_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/cellHTS_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/cellHTS_1.6.0.tgz vignettes: vignettes/cellHTS/inst/doc/cellhts.pdf, vignettes/cellHTS/inst/doc/twoChannels.pdf, vignettes/cellHTS/inst/doc/twoWay.pdf Package: cghMCR Version: 1.6.0 Depends: methods, DNAcopy, marray, arrayQuality Title: Find chromosome regions showing common gains/losses Description: Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform. biocViews: Platform, Microarray Author: J. Zhang and B. Feng Maintainer: J. Zhang License: LGPL source.ver: src/contrib/cghMCR_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/cghMCR_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/cghMCR_1.6.0.tgz vignettes: vignettes/cghMCR/inst/doc/findMCR.pdf Package: clusterStab Version: 1.8.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter Title: Compute cluster stability scores for microarray data Description: This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters. biocViews: Clustering Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin Maintainer: James W. MacDonald License: Artistic source.ver: src/contrib/clusterStab_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/clusterStab_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/clusterStab_1.8.0.tgz vignettes: vignettes/clusterStab/inst/doc/clusterStab.pdf Package: codelink Version: 1.4.0 Depends: methods, limma, annotate Title: Manipulation of Codelink Bioarrays data. Description: This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization. biocViews: Microarray, OneChannel, DataImport, Preprocessing Author: Diego Diez Maintainer: Diego Diez URL: http://www.kuicr.kyoto-u.ac.jp/~diez License: GPL source.ver: src/contrib/codelink_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/codelink_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/codelink_1.4.0.tgz vignettes: vignettes/codelink/inst/doc/codelink.pdf Package: convert Version: 1.10.0 Depends: R (>= 1.8.1), Biobase, limma (>= 1.7.0), marray, utils, methods Title: Convert Microarray Data Objects Description: Define coerce methods for microarray data objects. biocViews: Infrastructure, Microarray, TwoChannel Author: Gordon Smyth , James Wettenhall and Yee Hwa (Jean) Yang Maintainer: Yee Hwa (Jean) Yang URL: http://bioinf.wehi.edu.au/limma/convert.html License: LGPL source.ver: src/contrib/convert_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/convert_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/convert_1.10.0.tgz vignettes: vignettes/convert/inst/doc/convert.pdf Package: copa Version: 1.4.0 Depends: Biobase, methods Suggests: colonCA Title: Functions to perform cancer outlier profile analysis. Description: COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. biocViews: OneChannel, TwoChannel, DifferentialExpression, Visualization Author: James W. MacDonald Maintainer: James W. MacDonald License: Artistic source.ver: src/contrib/copa_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/copa_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/copa_1.4.0.tgz vignettes: vignettes/copa/inst/doc/copa.pdf Package: cosmoGUI Version: 1.2.0 Depends: tkWidgets, cosmo Title: GUI for constructing constraint sets used by the cosmo package Description: cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch. biocViews: SequenceMatching Author: Fabian Gallusser, Oliver Bembom, and Sandrine Dudoit Maintainer: Oliver Bembom URL: http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/ucbbiostat/paper209/ License: LGPL version 2 or newer source.ver: src/contrib/cosmoGUI_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/cosmoGUI_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/cosmoGUI_1.2.0.tgz Package: cosmo Version: 1.2.0 Depends: R (>= 2.4.0), methods, utils, seqLogo Suggests: cosmoGUI Title: Supervised detection of conserved motifs in DNA sequences Description: cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively. biocViews: SequenceMatching Author: Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit Maintainer: Oliver Bembom URL: http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/sagmb/vol6/iss1/art8 License: Free for research purposes only. For details, see COPYING or type license.cosmo() in R. source.ver: src/contrib/cosmo_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/cosmo_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/cosmo_1.2.0.tgz vignettes: vignettes/cosmo/inst/doc/cosmo.pdf Package: ctc Version: 1.10.0 Depends: amap Title: Cluster and Tree Conversion. Description: Tools for export and import classification trees and clusters to other programs biocViews: Microarray, Clustering, Classification, DataImport, Visualization Author: Antoine Lucas , Laurent Gautier Maintainer: Antoine Lucas URL: http://antoinelucas.free.fr/ctc License: GPL source.ver: src/contrib/ctc_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/ctc_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ctc_1.10.0.tgz vignettes: vignettes/ctc/inst/doc/ctc.pdf Package: daMA Version: 1.8.0 Depends: MASS Title: Efficient design and analysis of factorial two-colour microarray data Description: This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted) biocViews: Microarray, TwoChannel, Statistics, DifferentialExpression Author: Jobst Landgrebe and Frank Bretz Maintainer: Jobst Landgrebe URL: http://www.microarrays.med.uni-goettingen.de License: GPL version 2 or newer source.ver: src/contrib/daMA_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/daMA_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/daMA_1.8.0.tgz Package: diffGeneAnalysis Version: 1.18.0 Depends: minpack.lm (>= 1.0-4) Title: Performs differential gene expression Analysis Description: Analyze microarray data biocViews: Statistics, Microarray, DifferentialExpression Author: Choudary Jagarlamudi Maintainer: Choudary Jagarlamudi License: GPL source.ver: src/contrib/diffGeneAnalysis_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/diffGeneAnalysis_1.18.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/diffGeneAnalysis_1.18.0.tgz vignettes: vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf Package: ecolitk Version: 1.8.0 Depends: R (>= 2.5), affy, ecoliLeucine, ecolicdf, Biobase Suggests: graph, matchprobes, multtest, vsn Title: Meta-data and tools for E. coli Description: Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. biocViews: Annotation, Visualization Author: Laurent Gautier Maintainer: Laurent License: GPL version 2 or newer source.ver: src/contrib/ecolitk_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/ecolitk_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ecolitk_1.8.0.tgz vignettes: vignettes/ecolitk/inst/doc/ecolitk.pdf Package: edd Version: 1.14.0 Depends: methods, golubEsets, Biobase, class, nnet, xtable Title: expression density diagnostics Description: tools for evaluating cohort distributions of gene expression levels biocViews: Statistics, DifferentialExpression Author: Vince Carey Maintainer: Vince Carey License: LGPL source.ver: src/contrib/edd_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/edd_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/edd_1.14.0.tgz vignettes: vignettes/edd/inst/doc/HOWTO-edd.pdf, vignettes/edd/inst/doc/eddDetails.pdf Package: exonmap Version: 1.0.07 Depends: R (>= 2.0), affy, simpleaffy, genefilter, RColorBrewer, RMySQL (>= 0.5-11), DBI, methods, plier Title: High level analysis of Affymetrix exon array data Description: Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as fold-changes t-test and so on. Applies fine grained genome-wide annotation to the data. biocViews: Microarray, OneChannel, Preprocessing, Transcription, DataImport, Statistics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Michal Okoniewski, Tim Yates, Crispin J Miller Maintainer: Michal Okoniewski URL: http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk License: GPL version 2 or later source.ver: src/contrib/exonmap_1.0.07.tar.gz win.binary.ver: bin/windows/contrib/2.5/exonmap_1.0.07.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/exonmap_1.0.07.tgz vignettes: vignettes/exonmap/inst/doc/INSTALL.pdf, vignettes/exonmap/inst/doc/exonmap.example.pdf, vignettes/exonmap/inst/doc/exonmap.pdf Package: factDesign Version: 1.10.0 Depends: Biobase, affy, stats Title: Factorial designed microarray experiment analysis Description: This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. biocViews: Statistics, Microarray, DifferentialExpression Author: Denise Scholtens Maintainer: Denise Scholtens License: LGPL source.ver: src/contrib/factDesign_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/factDesign_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/factDesign_1.10.0.tgz vignettes: vignettes/factDesign/inst/doc/factDesign.pdf Package: fbat Version: 1.0.0 Depends: MASS Title: Family Based Association Tests for genetic data. Description: This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program (see http://www.biostat.harvard.edu/~fbat/fbat.htm). Features include: - Uses data from nuclear families, sibships, pedigrees, or any combination; provides unbiased tests with or without founder genotypes. - Analyzes dichotomous, measured, or time-to-onset traits and multiple traits; trait definition can be optimized. - Offers bi-allelic and multi-allelic tests of association using standard genetic models (additive, dominant, recessive or genotype). - Offers large sample and Monte-Carlo exact tests of the null hypothesis: no linkage and no association; offers large sample test of H0: no association. - Estimates allele frequencies; checks Mendelian consistency. - Tests multiple markers using haplotypes; estimates haplotype frequencies and linkage disequilibrium between pairs of markers. - Offers two multi-marker tests for testing multiple markers simultaneously, without resolving phase or assuming no recombination. - Uses standard pedigree data files; phenotype file is optional. - Offers the Sibs Disequilibrium Test. biocViews: Genetics Author: Weiliang Qiu Ross Lazarus Gregory Warnes Nitin Jain Maintainer: Weiliang Qiu License: LGPL source.ver: src/contrib/fbat_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/fbat_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/fbat_1.0.0.tgz vignettes: vignettes/fbat/inst/doc/fbat.pdf Package: fdrame Version: 1.8.0 Title: FDR adjustments of Microarray Experiments (FDR-AME) Description: This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma biocViews: Microarray,DifferentialExpression,MultipleComparisons Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli Maintainer: Effi Kenigsberg License: GPL Version 2 or later. source.ver: src/contrib/fdrame_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/fdrame_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/fdrame_1.8.0.tgz vignettes: vignettes/fdrame/inst/doc/fdrame.pdf Package: flowCore Version: 1.0.2 Depends: R (>= 2.4.0), Biobase, methods, rrcov Imports: Biobase, methods, geneplotter, graphics, graph, MASS, utils Title: flowCore: Basic structures for flow cytometry data Description: Provides S4 data structures and basic functions to deal with flow cytometry data. biocViews: Infrastructure, Flowcytometry, CellBasedAssays Author: B. Ellis, P. Haaland, F. Hahne, N. Le Meur Maintainer: Nolwenn Le Meur License: The Artistic License, Version 2.0 source.ver: src/contrib/flowCore_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.5/flowCore_1.0.2.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/flowCore_1.0.2.tgz vignettes: vignettes/flowCore/inst/doc/HowTo-flowCore.pdf Package: flowViz Version: 1.0.0 Depends: R (>= 2.4.0), flowCore (>= 0.3.0), Biobase, rgl, geneplotter, lattice, MASS, methods Title: Visualization for flow cytometry Description: Provides visualization tools for flow cytometry data. biocViews: Infrastructure, Flowcytometry, CellBasedAssays, Visualization Author: T. Duong, B. Ellis, R. Gentleman, F. Hahne, N. Le Meur, D. Sarkar, M. Tang Maintainer: Florian Hahne License: Artistic source.ver: src/contrib/flowViz_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/flowViz_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/flowViz_1.0.0.tgz Package: gaggle Version: 1.4.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2) Suggests: RUnit Title: Broadcast data between R and Java bioinformatics programs Description: this package contains functions connecting R with the Gaggle biocViews: Visualization, Annotation, GraphsAndNetworks Author: Paul Shannon Maintainer: Paul Shannon URL: http://gaggle.systemsbiology.org License: GPL version 2 or newer source.ver: src/contrib/gaggle_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/gaggle_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/gaggle_1.4.0.tgz vignettes: vignettes/gaggle/inst/doc/gaggle.pdf Package: gcrma Version: 2.8.1 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), matchprobes, splines Suggests: affydata Title: Background Adjustment Using Sequence Information Description: Background adjustment using sequence information biocViews: Microarray, OneChannel, Preprocessing Author: Jean(ZHIJIN) Wu, Rafael Irizarry with contributions from James MacDonald Jeff Gentry Maintainer: Z. Wu License: LGPL source.ver: src/contrib/gcrma_2.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/gcrma_2.8.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/gcrma_2.8.1.tgz vignettes: vignettes/gcrma/inst/doc/gcrma2.0.pdf Package: genArise Version: 1.12.0 Depends: R (>= 1.7.1), locfit, tkrplot, xtable, methods Title: Microarray Analysis tool Description: genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. biocViews: Microarray, TwoChannel, Preprocessing Author: Ana Patricia Gomez Mayen ,\\ Gustavo Corral Guille , \\ Lina Riego Ruiz ,\\ Gerardo Coello Coutino Maintainer: IFC Development Team URL: http://www.ifc.unam.mx/genarise License: Free for non-commercial use source.ver: src/contrib/genArise_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/genArise_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/genArise_1.12.0.tgz vignettes: vignettes/genArise/inst/doc/genArise.pdf Package: geneRecommender Version: 1.8.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22) Title: A gene recommender algorithm to identify genes coexpressed with a query set of genes Description: This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. biocViews: Microarray, Clustering Author: Gregory J. Hather , with contributions from Art B. Owen and Terence P. Speed Maintainer: Greg Hather License: GPL version 2 or newer source.ver: src/contrib/geneRecommender_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/geneRecommender_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/geneRecommender_1.8.0.tgz vignettes: vignettes/geneRecommender/inst/doc/geneRecommender.pdf Package: genefilter Version: 1.14.1 Depends: R (>= 2.1.0), methods, Biobase, survival Imports: annotate (>= 1.13.7) Suggests: class, hgu95av2, tkWidgets Title: genefilter: methods for filtering genes from microarray experiments Description: Some basic functions for filtering genes biocViews: Statistics, Microarray Author: R. Gentleman, V. Carey, W. Huber, F. Hahne Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/genefilter_1.14.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/genefilter_1.14.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/genefilter_1.14.1.tgz vignettes: vignettes/genefilter/inst/doc/howtogenefilter.pdf, vignettes/genefilter/inst/doc/howtogenefinder.pdf Package: geneplotter Version: 1.14.0 Depends: R (>= 2.4.0), annotate, Biobase (>= 1.11.34), methods, lattice Imports: KernSmooth, RColorBrewer Suggests: Rgraphviz, hgu95av2, fibroEset, hu6800, hgu133a, GO, KernSmooth, RColorBrewer Title: Grapics related functions for Bioconductor Description: Some basic functions for plotting genetic data biocViews: Visualization Author: R. Gentleman, Biocore Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/geneplotter_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/geneplotter_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/geneplotter_1.14.0.tgz vignettes: vignettes/geneplotter/inst/doc/byChroms.pdf, vignettes/geneplotter/inst/doc/visualize.pdf Package: globaltest Version: 4.6.0 Depends: R, methods, graphics, multtest Imports: Biobase, survival, annotate Suggests: vsn, golubEsets, KEGG, hu6800, GOstats, Rgraphviz, GO Title: Testing Association of Groups of Genes with a Clinical Variable Description: Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest. biocViews: Microarray, OneChannel, Statistics, DifferentialExpression, GO, Pathways Author: Jelle Goeman and Jan Oosting Maintainer: Jelle Goeman URL: http://www.msbi.nl/goeman License: GPL version 2 or newer source.ver: src/contrib/globaltest_4.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/globaltest_4.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/globaltest_4.6.0.tgz vignettes: vignettes/globaltest/inst/doc/GlobalTest.pdf Package: goTools Version: 1.8.0 Depends: Biobase, annotate, GO Suggests: hgu133a Title: Functions for Gene Ontology database Description: Wraper functions for description/comparison of oligo ID list using Gene Ontology database biocViews: Microarray,GO,Visualization Author: Yee Hwa (Jean) Yang , Agnes Paquet Maintainer: Agnes Paquet License: GPL2 source.ver: src/contrib/goTools_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/goTools_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/goTools_1.8.0.tgz vignettes: vignettes/goTools/inst/doc/goTools.pdf Package: gpls Version: 1.8.0 Title: Classification using generalized partial least squares Description: Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification. biocViews: Statistics, Classification, Microarray Author: Beiying Ding Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/gpls_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/gpls_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/gpls_1.8.0.tgz vignettes: vignettes/gpls/inst/doc/gpls.pdf Package: graph Version: 1.14.2 Depends: R (>= 2.5.0), methods Imports: cluster, methods Suggests: SparseM (>= 0.36), XML, RBGL Title: graph: A package to handle graph data structures Description: A package that implements some simple graph handling capabilities. biocViews: GraphsAndNetworks Author: R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon Maintainer: Seth Falcon License: The Artistic License, Version 2.0 source.ver: src/contrib/graph_1.14.2.tar.gz win.binary.ver: bin/windows/contrib/2.5/graph_1.14.2.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/graph_1.14.2.tgz vignettes: vignettes/graph/inst/doc/clusterGraph.pdf, vignettes/graph/inst/doc/graph.pdf, vignettes/graph/inst/doc/graphAttributes.pdf Package: hexbin Version: 1.10.0 Depends: R (>= 2.0), methods, grid, lattice Suggests: marray, cluster, affy, Biobase Title: Hexagonal Binning Routines Description: Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods. biocViews: Visualization Author: Dan Carr , ported by Nicholas Lewin-Koh and Martin Maechler Maintainer: Nicholas Lewin-Koh License: GPL 2 source.ver: src/contrib/hexbin_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/hexbin_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/hexbin_1.10.0.tgz vignettes: vignettes/hexbin/inst/doc/hexagon_binning.pdf Package: hopach Version: 1.10.0 Depends: R (>= 1.8.0), cluster, Biobase Title: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) Description: The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). biocViews: Clustering Author: Katherine S. Pollard, with Mark J. van der Laan . Maintainer: Katherine S. Pollard URL: http://www.r-project.org, http://www.stat.berkeley.edu/~laan/, http://docpollard.com/ License: GPL version 2 or newer source.ver: src/contrib/hopach_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/hopach_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/hopach_1.10.0.tgz vignettes: vignettes/hopach/inst/doc/MSS.pdf, vignettes/hopach/inst/doc/bootplot.pdf, vignettes/hopach/inst/doc/dplot.pdf, vignettes/hopach/inst/doc/hopach.pdf, vignettes/hopach/inst/doc/hopachManuscript.pdf Package: hypergraph Version: 1.8.0 Depends: R (>= 2.1.0), methods, graph Title: A package providing hypergraph data structures Description: A package that implements some simple capabilities for representing and manipulating hypergraphs. biocViews: Infrastructure, GraphsAndNetworks Author: Seth Falcon, Robert Gentleman Maintainer: Seth Falcon License: LGPL source.ver: src/contrib/hypergraph_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/hypergraph_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/hypergraph_1.8.0.tgz Package: iSNetwork Version: 1.6.0 Depends: R (>= 2.0.0), methods, graph, Rgraphviz, RGtk, gtkDevice, BioMVCClass, MVCClass, Biobase, annotate (>= 1.11.10) Imports: methods Suggests: genefilter, Category, GOstats Title: Interactive Network Plots Description: Allows the user to interact with plots of networks. biocViews: GraphsAndNetworks, Visualization Author: Elizabeth Whalen Maintainer: Elizabeth Whalen License: LGPL source.ver: src/contrib/iSNetwork_1.6.0.tar.gz mac.binary.ver: bin/macosx/universal/contrib/2.5/iSNetwork_1.6.0.tgz vignettes: vignettes/iSNetwork/inst/doc/iSNetwork.pdf Package: iSPlot Version: 1.10.0 Depends: R (>= 2.0.0), methods, RGtk, gtkDevice, MVCClass Title: Linking Plots Description: Allows the user to link views that are based on the same data set. biocViews: Visualization Author: Elizabeth Whalen Maintainer: Elizabeth Whalen License: LGPL source.ver: src/contrib/iSPlot_1.10.0.tar.gz mac.binary.ver: bin/macosx/universal/contrib/2.5/iSPlot_1.10.0.tgz vignettes: vignettes/iSPlot/inst/doc/iSPlot.pdf Package: idiogram Version: 1.10.0 Depends: R (>= 2.0.0), methods, Biobase, annotate Title: idiogram Description: A package for plotting genomic data by chromosomal location biocViews: Visualization Author: Kyle A. Furge Maintainer: Karl J. Dykema License: GPL2 source.ver: src/contrib/idiogram_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/idiogram_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/idiogram_1.10.0.tgz vignettes: vignettes/idiogram/inst/doc/idiogram.pdf Package: impute Version: 1.8.0 Depends: R (>= 1.7.0) Title: impute: Imputation for microarray data Description: Imputation for microarray data (currently KNN only) biocViews: Statistics, Microarray Author: Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu Maintainer: Balasubramanian Narasimhan License: GPL2.0 source.ver: src/contrib/impute_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/impute_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/impute_1.8.0.tgz Package: lapmix Version: 1.2.0 Depends: R Title: Laplace Mixture Model in Microarray Experiments Description: Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes. biocViews: Statistics, Microarray, OneChannel, DifferentialExpression Author: Yann Ruffieux, contributions from Debjani Bhowmick, Anthony C. Davison, and Darlene R. Goldstein Maintainer: Yann Ruffieux URL: http://www.r-project.org, http://www.bioconductor.org, http://stat.epfl.ch License: GPL version 2 or newer source.ver: src/contrib/lapmix_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/lapmix_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/lapmix_1.2.0.tgz vignettes: vignettes/lapmix/inst/doc/lapmix-example.pdf Package: limmaGUI Version: 1.12.0 Depends: limma, tcltk Suggests: statmod, sma, R2HTML, xtable, tkrplot Title: GUI for limma package Description: A Graphical User Interface for the limma Microarray package biocViews: Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, Statistics, DifferentialExpression, MultipleComparisons Author: James Wettenhall Division of Genetics and Bioinformatics, WEHI Maintainer: Keith Satterley URL: http://bioinf.wehi.edu.au/limmaGUI/ License: LGPL source.ver: src/contrib/limmaGUI_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/limmaGUI_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/limmaGUI_1.12.0.tgz vignettes: vignettes/limmaGUI/inst/doc/LinModIntro.pdf, vignettes/limmaGUI/inst/doc/extract.pdf, vignettes/limmaGUI/inst/doc/limmaGUI.pdf Package: limma Version: 2.10.5 Depends: R (>= 2.3.0), methods Suggests: affy, marray, MASS, splines, sma, statmod (>= 1.2.2), vsn Title: Linear Models for Microarray Data Description: Data analysis, linear models and differential expression for microarray data. biocViews: Microarray, OneChannel, TwoChannel, DataImport, QualityControl, Preprocessing, Statistics, DifferentialExpression, MultipleComparisons, TimeCourse Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin and Dongseok Choi. Maintainer: Gordon Smyth URL: http://bioinf.wehi.edu.au/limma License: LGPL source.ver: src/contrib/limma_2.10.5.tar.gz win.binary.ver: bin/windows/contrib/2.5/limma_2.10.5.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/limma_2.10.5.tgz vignettes: vignettes/limma/inst/doc/limma.pdf, vignettes/limma/inst/doc/usersguide.pdf Package: logicFS Version: 1.6.0 Depends: LogicReg Title: Identification of SNP Interactions Description: Identification of interactions between binary variables using LogiC Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a first basic bagging version of logic regression for classification. biocViews: SNPsAndGeneticVariability, FeatureSelection, Classification Author: Holger Schwender Maintainer: Holger Schwender License: LGPL version 2 or newer source.ver: src/contrib/logicFS_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/logicFS_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/logicFS_1.6.0.tgz vignettes: vignettes/logicFS/inst/doc/logicFS.pdf Package: lumi Version: 1.2.0 Depends: R (>= 2.4.0), Biobase (>= 1.12.0), affy, mgcv, annotate, methods Suggests: vsn Title: BeadArray Specific Methods for Illumina Microarrays Description: The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. biocViews: Microarray, OneChannel, Preprocessing Author: Pan Du, Warren Kibbe, Simon Lin Maintainer: Pan Du License: LGPL version 2 or newer source.ver: src/contrib/lumi_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/lumi_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/lumi_1.2.0.tgz vignettes: vignettes/lumi/inst/doc/lumi.pdf Package: maCorrPlot Version: 1.6.0 Depends: lattice Title: Visualize artificial correlation in microarray data Description: Graphically displays correlation in microarray data that is due to insufficient normalization biocViews: Microarray, Preprocessing, Visualization Author: Alexander Ploner Maintainer: Alexander Ploner URL: http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15799785 License: GPL2 or later source.ver: src/contrib/maCorrPlot_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/maCorrPlot_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/maCorrPlot_1.6.0.tgz vignettes: vignettes/maCorrPlot/inst/doc/maCorrPlot.pdf Package: maDB Version: 1.8.1 Depends: R (>= 2.5.0), Biobase (>= 1.14.0), affy (>= 1.6.0), pgUtils (>= 1.5.0), limma (>= 1.8.0), methods Suggests: geneplotter (>= 1.6.0), annaffy (>= 1.6.2), biomaRt (>= 1.8.2) Title: Microarray database and utility functions for microarray data analysis. Description: maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays. biocViews: Microarray,TwoChannel,OneChannel,Visualization Author: Johannes Rainer Maintainer: Johannes Rainer License: LGPL version 2 or newer source.ver: src/contrib/maDB_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/maDB_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/maDB_1.8.0.tgz vignettes: vignettes/maDB/inst/doc/maDB.pdf Package: maSigPro Version: 2.0.1 Depends: R (>= 2.3.1), Biobase Suggests: marray, EMV, limma, Mfuzz Title: Significant Gene Expression Profile Differeneces in Time Course Microarray Data Description: maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments. biocViews: Microarray, DifferentialExpression, TimeCourse Author: Ana Conesa , Maria Jose Nueda Maintainer: Ana Conesa URL: http://bioinfo.cipf.es/ License: GPL (version 2 or newer) source.ver: src/contrib/maSigPro_2.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/maSigPro_2.0.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/maSigPro_2.0.1.tgz vignettes: vignettes/maSigPro/inst/doc/maSigPro-tutorial.pdf, vignettes/maSigPro/inst/doc/maSigPro.pdf Package: maanova Version: 1.6.0 Depends: R (>= 2.3.0) Suggests: snow Title: Tools for analyzing Micro Array experiments Description: Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree. biocViews: Microarray, DifferentialExpression, Clustering Author: Hao Wu, with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui Maintainer: Lei Wu URL: http://www.jax.org/staff/churchill/labsite/software/Rmaanova/ License: GPL version 2 or later source.ver: src/contrib/maanova_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/maanova_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/maanova_1.6.0.tgz vignettes: vignettes/maanova/inst/doc/abf1.pdf, vignettes/maanova/inst/doc/hckidney.pdf, vignettes/maanova/inst/doc/maanova.pdf, vignettes/maanova/inst/doc/paigen.pdf, vignettes/maanova/inst/doc/vgprofile.pdf Package: macat Version: 1.10.0 Depends: Biobase, annotate Suggests: hgu95av2, stjudem Title: MicroArray Chromosome Analysis Tool Description: This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'. biocViews: Microarray, DifferentialExpression, Visualization Author: Benjamin Georgi, Matthias Heinig, Stefan Roepcke, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling License: Artistic License 2.0 source.ver: src/contrib/macat_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/macat_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/macat_1.10.0.tgz vignettes: vignettes/macat/inst/doc/Slidingchrom6s3.pdf, vignettes/macat/inst/doc/chrom6T.pdf, vignettes/macat/inst/doc/chrom6TkNN.pdf, vignettes/macat/inst/doc/evalkNN6.pdf, vignettes/macat/inst/doc/macat.pdf Package: made4 Version: 1.10.1 Depends: ade4, scatterplot3d Suggests: affy,RColorBrewer Title: Multivariate analysis of microarray data using ADE4 Description: Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4. biocViews: Statistics, Clustering, Classification, MultipleComparisons Author: Aedin Culhane Maintainer: Aedin Culhane URL: http://www.hsph.harvard.edu/researchers/aculhane.html License: Artistic licence source.ver: src/contrib/made4_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/made4_1.10.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/made4_1.10.1.tgz vignettes: vignettes/made4/inst/doc/html3D.pdf, vignettes/made4/inst/doc/introduction.pdf Package: makePlatformDesign Version: 1.0.0 Depends: affyio, oligo Title: Platform Design Package Description: makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo. biocViews: OneChannel, TwoChannel, Microarray, Preprocessing Author: Benilton Carvalho , Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber Maintainer: Benilton Carvalho License: LGPL version 2 or newer source.ver: src/contrib/makePlatformDesign_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/makePlatformDesign_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/makePlatformDesign_1.0.0.tgz Package: makecdfenv Version: 1.14.0 Depends: R (>= 2.1.0), methods, Biobase (>= 1.4.1), affy (>= 1.4.0), utils, affyio Title: CDF Environment Maker Description: This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. biocViews: OneChannel, DataImport, Preprocessing Author: Rafael A. Irizarry , Laurent Gautier , Wolfgang Huber , Ben Bolstad Maintainer: James W. MacDonald License: GPL version 2 or newer source.ver: src/contrib/makecdfenv_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/makecdfenv_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/makecdfenv_1.14.0.tgz vignettes: vignettes/makecdfenv/inst/doc/makecdfenv.pdf Package: marray Version: 1.14.0 Depends: R (>= 1.9.0), limma, methods, tkWidgets Title: Exploratory analysis for two-color spotted microarray data Description: Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. biocViews: Microarray, TwoChannel, Preprocessing Author: Yee Hwa (Jean) Yang with contributions from Agnes Paquet and Sandrine Dudoit. Maintainer: Yee Hwa (Jean) Yang URL: http://www.maths.usyd.edu.au/u/jeany/ License: LGPL source.ver: src/contrib/marray_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/marray_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/marray_1.14.0.tgz vignettes: vignettes/marray/inst/doc/ExampleHTML.pdf, vignettes/marray/inst/doc/marray.pdf, vignettes/marray/inst/doc/marrayClasses.pdf, vignettes/marray/inst/doc/marrayClassesShort.pdf, vignettes/marray/inst/doc/marrayInput.pdf, vignettes/marray/inst/doc/marrayNorm.pdf, vignettes/marray/inst/doc/marrayPlots.pdf, vignettes/marray/inst/doc/widget1.pdf Package: matchprobes Version: 1.8.1 Depends: R (>= 2.3.0), Biobase (>= 1.6.0), affy Suggests: hgu95av2cdf, hgu95av2probe, hu6800cdf, hu6800probe Title: Tools for sequence matching of probes on arrays Description: Tools for sequence matching of probes on arrays biocViews: Microarray, Annotation Author: Robert Gentleman, Wolfgang Huber Maintainer: Biocore Team License: The Artistic License, Version 2.0 source.ver: src/contrib/matchprobes_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/matchprobes_1.8.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/matchprobes_1.8.1.tgz vignettes: vignettes/matchprobes/inst/doc/matchprobes.pdf Package: metaArray Version: 1.10.0 Depends: MergeMaid Title: Integration of Microarray Data for Meta-analysis Description: 1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform biocViews: Microarray, Statistics, DifferentialExpression Author: Debashis Ghosh Hyungwon Choi Maintainer: Hyungwon Choi License: LGPL2 source.ver: src/contrib/metaArray_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/metaArray_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/metaArray_1.10.0.tgz vignettes: vignettes/metaArray/inst/doc/metaArray.pdf Package: multtest Version: 1.14.0 Depends: R (>= 2.1.0), methods, Biobase, survival Title: Resampling-based multiple hypothesis testing Description: Non-parametric bootstrap and permutation resampling-based multiple testing procedures for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Single-step and step-wise methods are implemented. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models) are included. Results are reported in terms of adjusted p-values, confindence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. biocViews: Microarray, DifferentialExpression, MultipleComparisons Author: Katherine S. Pollard, Yongchao Ge, Sandrine Dudoit Maintainer: Katherine S. Pollard License: LGPL source.ver: src/contrib/multtest_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/multtest_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/multtest_1.14.0.tgz vignettes: vignettes/multtest/inst/doc/MTP.pdf, vignettes/multtest/inst/doc/MTPALL.pdf, vignettes/multtest/inst/doc/multtest.pdf Package: nem Version: 1.6.0 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.10), Rgraphviz (>= 1.10), RBGL (>= 1.8.1), time (>= 1.0) Suggests: Biobase (>= 1.10) Title: Nested Effects Models to reconstruct phenotypic hierarchies Description: The package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) high-dimensional phenotypic readout of these perturbations (e.g. gene expression or morphological profiles). The output is a directed graph representing the phenotypic hierarchy. biocViews: Microarray, Statistics, GraphsAndNetworks, Pathways Author: Florian Markowetz, Holger Froehlich, Matthias Maneck, with contributions from Tim Beissbarth and Claudio Lottaz Maintainer: Florian Markowetz URL: http://www.bioconductor.org License: GPL version 2.0 or newer source.ver: src/contrib/nem_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/nem_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/nem_1.6.0.tgz vignettes: vignettes/nem/inst/doc/markowetz-thesis-2006.pdf, vignettes/nem/inst/doc/nem.pdf Package: nnNorm Version: 2.0.0 Depends: R(>= 2.2.0), nnet, marray Title: Spatial and intensity based normalization of cDNA microarray data based on robust neural nets Description: This package allows to detect and correct for spatial and intensity biases. The normalization method implemented in this package is based on robust neural networks fitting. biocViews: Microarray, TwoChannel, Preprocessing Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca License: LGPL source.ver: src/contrib/nnNorm_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/nnNorm_2.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/nnNorm_2.0.0.tgz vignettes: vignettes/nnNorm/inst/doc/nnNorm.pdf, vignettes/nnNorm/inst/doc/nnNormGuide.pdf Package: oligo Version: 1.0.2-6 Depends: methods, R (>= 2.5.0), Biobase (>= 1.13.58), affyio (>= 1.3.4), splines, RSQLite, BufferedMatrix (>= 0.99.00), BufferedMatrixMethods (>= 0.99.0) Suggests: hapmap100kxba, pd.mapping50k.xba240, geneplotter Title: Oligonucleotide Arrays Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. biocViews: Microarray, OneChannel, TwoChannel, Preprocessing Author: Benilton Carvalho , Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber Maintainer: Benilton Carvalho License: LGPL version 2 or newer source.ver: src/contrib/oligo_1.0.2-6.tar.gz win.binary.ver: bin/windows/contrib/2.5/oligo_1.0.2-3.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/oligo_1.0.2-6.tgz vignettes: vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf, vignettes/oligo/inst/doc/oligo.pdf Package: oneChannelGUI Version: 1.2.20 Depends: Biobase, affylmGUI, tkWidgets Suggests: annotate, GOstats, genefilter, maSigPro, pamr, pdmclass, Rgraphviz, affy ,annaffy, affyPLM, multtest, ssize, sizepower, siggenes, RankProd, humanLLMappings, mouseLLMappings, ratLLMappings, metaArray Title: This package extends the capabilities of affylmGUI graphical interface. Description: This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface allowing QC, filtering, statistical validation, and alternative splicing analysis. Affymetrix 3' IVT, Human Gene 1.0 ST and exon arrays are actually implemented. biocViews: Microarray, OneChannel, DataImport, QualityControl, Preprocessing, Statistics, DifferentialExpression, MultipleComparisons Author: Raffale A Calogero, Bioinformatics and Genomics Unit, Dept. of Clinical and Biological Sciences Torino (Italy) Maintainer: Raffaele A Calogero URL: http://www.bioinformatica.unito.it/oneChannelGUI/ License: The Artistic License, Version 2.0 source.ver: src/contrib/oneChannelGUI_1.2.20.tar.gz win.binary.ver: bin/windows/contrib/2.5/oneChannelGUI_1.2.20.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/oneChannelGUI_1.2.2.tgz vignettes: vignettes/oneChannelGUI/inst/doc/fignew42.pdf, vignettes/oneChannelGUI/inst/doc/install.pdf, vignettes/oneChannelGUI/inst/doc/oneChannelGUI.pdf Package: ontoTools Version: 1.12.1 Depends: R (>= 2.4.0), methods, graph, SparseM, GO, Biobase, annotate Suggests: combinat, Iyer517, humanLLMappings Title: graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management Description: tools for working with ontologies and graphs biocViews: GraphsAndNetworks, Infrastructure Author: Vince Carey Maintainer: Vince Carey License: GPL2 source.ver: src/contrib/ontoTools_1.12.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/ontoTools_1.12.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ontoTools_1.12.1.tgz vignettes: vignettes/ontoTools/inst/doc/demoComp.pdf, vignettes/ontoTools/inst/doc/ontoTools.pdf, vignettes/ontoTools/inst/doc/ontoToolsArchiving.pdf, vignettes/ontoTools/inst/doc/prot2.pdf, vignettes/ontoTools/inst/doc/protlk.pdf, vignettes/ontoTools/inst/doc/sgdiOnto.pdf Package: pamr Version: 1.34.0 Depends: cluster, survival Title: Pam: prediction analysis for microarrays Description: Some functions for sample classification in microarrays biocViews: Classification, Microarray Author: T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu Maintainer: Rob Tibshirani License: GPL2.0 source.ver: src/contrib/pamr_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/pamr_1.34.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/pamr_1.34.0.tgz Package: panp Version: 1.7.1 Depends: affy (>= 1.14.0), R (>= 2.5.0), Biobase (>= 1.14.0) Title: Presence-Absence Calls from Negative Strand Matching Probesets Description: A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. biocViews: Microarray, OneChannel, Transcription Author: Peter Warren Maintainer: Peter Warren License: GPL version 2 or newer source.ver: src/contrib/panp_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/panp_1.7.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/panp_1.7.1.tgz vignettes: vignettes/panp/inst/doc/panp.pdf Package: pathRender Version: 1.4.0 Depends: graph, Rgraphviz, cMAP Title: Render molecular pathways Description: build graphs from pathway databases, render them by Rgraphviz biocViews: GraphsAndNetworks Author: Li Long Maintainer: Li Long URL: http://www.bioconductor.org License: LGPL source.ver: src/contrib/pathRender_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/pathRender_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/pathRender_1.4.0.tgz Package: pcaMethods Version: 1.12.0 Depends: R, MASS, pls, methods Suggests: aroma.light Title: A collection of PCA methods. Description: Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimationn is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a unique interface to the PCA results. Developed at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany. biocViews: Statistics Author: Wolfram Stacklies, Henning Redestig Maintainer: Wolfram Stacklies License: GPL version 2 (or later) source.ver: src/contrib/pcaMethods_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/pcaMethods_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/pcaMethods_1.12.0.tgz vignettes: vignettes/pcaMethods/inst/doc/missingValues.pdf, vignettes/pcaMethods/inst/doc/outliers.pdf, vignettes/pcaMethods/inst/doc/pcaMethods.pdf Package: pcot2 Version: 1.4.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800, KEGG, mvtnorm Title: Principle Coordinates and Hotelling's T-Square method Description: PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons. biocViews: Microarray, DifferentialExpression Author: Sarah Song, Mik Black Maintainer: Sarah Song License: GPL version 2 or newer source.ver: src/contrib/pcot2_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/pcot2_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/pcot2_1.4.0.tgz vignettes: vignettes/pcot2/inst/doc/HowToUseGeneLocator.pdf, vignettes/pcot2/inst/doc/pcot2.pdf Package: pdInfoBuilder Version: 1.0.0 Depends: R (>= 2.5.0), methods, Biobase (>= 1.13.17), RSQLite (>= 0.4-15), affxparser (>= 1.7.2), oligo (>= 0.99.97) Title: Platform Design Information Package Builder Description: Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. munged vc for Cytoband biocViews: Annotation, Infrastructure Author: Seth Falcon Maintainer: Seth Falcon License: The Artistic License, Version 2.0 source.ver: src/contrib/pdInfoBuilder_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/pdInfoBuilder_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/pdInfoBuilder_1.0.0.tgz vignettes: vignettes/pdInfoBuilder/inst/doc/howto-AffymetrixMapping.pdf Package: pdmclass Version: 1.8.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda Title: Classification of Microarray Samples using Penalized Discriminant Methods Description: This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression. biocViews: Classification Author: James W. MacDonald, Debashis Ghosh, based in part on pls code of Mike Denham Maintainer: James W. MacDonald License: Artistic source.ver: src/contrib/pdmclass_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/pdmclass_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/pdmclass_1.8.0.tgz vignettes: vignettes/pdmclass/inst/doc/pdmclass.pdf Package: pgUtils Version: 1.8.0 Depends: R (>= 1.8.0), Rdbi (>= 1.0.2), RdbiPgSQL (>= 1.0.2), methods Title: Utility functions for PostgreSQL databases Description: Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism. biocViews: Infrastructure Author: Johannes Rainer Maintainer: Johannes Rainer License: LGPL version 2 or newer source.ver: src/contrib/pgUtils_1.8.0.tar.gz vignettes: vignettes/pgUtils/inst/doc/pgUtils.pdf Package: pickgene Version: 1.8.0 Depends: MASS Title: Adaptive Gene Picking for Microarray Expression Data Analysis Description: Functions to Analyze Microarray (Gene Expression) Data. biocViews: Microarray, DifferentialExpression Author: Brian S. Yandell Maintainer: Brian S. Yandell URL: http://www.stat.wisc.edu/~yandell/statgen License: GPL version 2 or newer source.ver: src/contrib/pickgene_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/pickgene_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/pickgene_1.8.0.tgz vignettes: vignettes/pickgene/inst/doc/pickgene.pdf Package: pkgDepTools Version: 1.2.1 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl Title: Package Dependency Tools Description: This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained. biocViews: Infrastructure, GraphsAndNetworks Author: Seth Falcon Maintainer: Seth Falcon License: GPL2 source.ver: src/contrib/pkgDepTools_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/pkgDepTools_1.2.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/pkgDepTools_1.2.1.tgz vignettes: vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf Package: plgem Version: 1.8.0 Depends: R (>= 1.9.0), Biobase, MASS Title: Power Law Global Error Model Description: PLGEM is useful for detecting differential expression in microarray datasets. biocViews: Microarray, DifferentialExpression Author: Mattia Pelizzola and Norman Pavelka Maintainer: Mattia Pelizzola URL: http://www.genopolis.it License: GPL source.ver: src/contrib/plgem_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/plgem_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/plgem_1.8.0.tgz vignettes: vignettes/plgem/inst/doc/plgem.pdf Package: plier Version: 1.6.0 Depends: R (>= 2.0), affy, methods Title: Implements the Affymetrix PLIER algorithm Description: The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. Author: Affymetrix Inc., Crispin J Miller, PICR Maintainer: Crispin Miller License: GPL version 2 or later source.ver: src/contrib/plier_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/plier_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/plier_1.6.0.tgz Package: ppiStats Version: 1.2.0 Depends: GO, GOstats, YEAST, graph, Category, ppiData (>= 0.1.1) Suggests: yeastExpData, Matrix, geneplotter, lattice, grid, xtable, Biobase, RColorBrewer Title: Protein-Protein Interaction Statistical Package Description: Package to analyze Bait to Prey Data Sets biocViews: Proteomics, GraphsAndNetworks Author: Tony Chiang Maintainer: Tony Chiang License: LGPL source.ver: src/contrib/ppiStats_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/ppiStats_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ppiStats_1.2.0.tgz vignettes: vignettes/ppiStats/inst/doc/supp.pdf Package: prada Version: 1.12.0 Depends: R (>= 2.1.0), Biobase, RColorBrewer, grid, methods Imports: MASS, KernSmooth, RColorBrewer, geneplotter, rrcov Suggests: cellHTS, rflowcyt Title: Data analysis for cell-based functional assays Description: Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy). biocViews: CellBasedAssays, Visualization Author: Florian Hahne , Wolfgang Huber , Markus Ruschhaupt , Joern Toedling Maintainer: Florian Hahne URL: http://www.dkfz.de/mga/whuber, http://www.dkfz.de/LIFEdb License: LPGL source.ver: src/contrib/prada_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/prada_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/prada_1.12.0.tgz vignettes: vignettes/prada/inst/doc/norm2.pdf, vignettes/prada/inst/doc/prada2cellHTS.pdf Package: puma Version: 1.2.3 Depends: R (>= 2.5.0), Biobase, affy, limma, annotate, ROCR Suggests: pumadata, methods, snow Title: Propagating Uncertainty in Microarray Analysis Description: Most analyses of Affymetrix GeneChip data 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. 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 and data manipulation functions. biocViews: Microarray, OneChannel, Preprocessing, Statistics, DifferentialExpression, Clustering Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti Maintainer: Richard Pearson URL: http://umber.sbs.man.ac.uk/resources/puma License: LGPL excluding donlp2 source.ver: src/contrib/puma_1.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.5/puma_1.2.3.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/puma_1.2.3.tgz vignettes: vignettes/puma/inst/doc/puma.pdf Package: quantsmooth Version: 1.2.0 Depends: quantreg, lodplot Title: Quantile smoothing and genomic visualization of array data Description: Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53. biocViews: Visualization, DNACopyNumber Author: Jan Oosting, Paul Eilers, Renee Menezes Maintainer: Jan Oosting License: GPL V2 source.ver: src/contrib/quantsmooth_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/quantsmooth_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/quantsmooth_1.2.0.tgz vignettes: vignettes/quantsmooth/inst/doc/quantsmooth.pdf Package: qvalue Version: 1.10.0 Depends: R (>= 1.7.0) Title: Q-value estimation for false discovery rate control Description: This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. biocViews: MultipleComparisons Author: Alan Dabney and John D. Storey , with assistance from Gregory R. Warnes Maintainer: John D. Storey License: LGPL source.ver: src/contrib/qvalue_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/qvalue_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/qvalue_1.10.0.tgz vignettes: vignettes/qvalue/inst/doc/manual.pdf, vignettes/qvalue/inst/doc/pHist.pdf, vignettes/qvalue/inst/doc/qHist.pdf, vignettes/qvalue/inst/doc/qPlots.pdf, vignettes/qvalue/inst/doc/qvalue-002.pdf, vignettes/qvalue/inst/doc/qvalue-004.pdf, vignettes/qvalue/inst/doc/qvalue-006.pdf, vignettes/qvalue/inst/doc/qvalue.pdf Package: rHVDM Version: 1.2.0 Depends: R (>= 2.3), R2HTML (>= 1.5), affy (>= 1.5), minpack.lm (>= 1.0), Biobase Title: Hidden Variable Dynamic Modeling Description: A R implementation of HVDM (Genome Biol 2006, V7(3) R25) biocViews: Microarray, GraphsAndNetworks, Transcription, Classification Author: Martino Barenco Maintainer: Martino Barenco License: GPL version 2.0 or later source.ver: src/contrib/rHVDM_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/rHVDM_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/rHVDM_1.2.0.tgz vignettes: vignettes/rHVDM/inst/doc/rHVDM.pdf Package: rama Version: 1.8.0 Title: Robust Analysis of MicroArrays Description: Robust estimation of cDNA microarray intensities with replicates. The package uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance. biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Raphael Gottardo Maintainer: Raphael Gottardo License: GPL version 2 or newer source.ver: src/contrib/rama_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/rama_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/rama_1.8.0.tgz Package: rbsurv Version: 1.2.0 Depends: R (>= 2.4.0), Biobase, survival Title: Robust likelihood-based survival modeling with microarray data Description: This package selects genes associated with survival. biocViews: Microarray, Statistics Author: HyungJun Cho , Sukwoo Kim , Jaewoo Kang , Jae Won Lee Maintainer: Sukwoo Kim URL: http://www.korea.ac.kr/~stat2242/ License: GPL version 2 or newer source.ver: src/contrib/rbsurv_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/rbsurv_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/rbsurv_1.2.0.tgz vignettes: vignettes/rbsurv/inst/doc/rbsurv.pdf Package: reb Version: 1.10.1 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) Title: Regional Expression Biases Description: A set of functions to dentify regional expression biases biocViews: Microarray, DNACopyNumber, Visualization Author: Kyle A. Furge and Karl Dykema Maintainer: Karl J. Dykema License: VAI, Free for non-commercial, academic use. source.ver: src/contrib/reb_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/reb_1.10.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/reb_1.10.1.tgz vignettes: vignettes/reb/inst/doc/reb.pdf Package: rflowcyt Version: 1.8.0 Depends: R (>= 2.3.0), survival, xtable, stats, KernSmooth, MASS, grid, methods, hexbin, rfcdmin (>= 0.9.0), fields, lattice, locfit, splancs Imports: prada, graphics Suggests: prada, xgobi Title: Statistical tools and data structures for analytic flow cytometry Description: Provides basic S4 data structures and routines for analysing flow cytometry data. biocViews: Statistics, Infrastructure, CellBasedAssays Author: A.J. Rossini, J.Y. Wan, N. LeMeur and Zoe Moodie Maintainer: N. LeMeur License: GNU General Public License 2.0. source.ver: src/contrib/rflowcyt_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/rflowcyt_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/rflowcyt_1.8.0.tgz vignettes: vignettes/rflowcyt/inst/doc/rflowcyt.pdf Package: safe Version: 1.8.0 Depends: R (>= 2.0.0), methods, Biobase Suggests: multtest, hu6800 Title: Significance Analysis of Function and Expression Description: SAFE is a permutation-based method for testing functional categories is gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions. biocViews: Microarray, DifferentialExpression Author: William T. Barry Maintainer: William T. Barry License: GPL version 2 or newer source.ver: src/contrib/safe_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/safe_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/safe_1.8.0.tgz vignettes: vignettes/safe/inst/doc/SAFEmanual.pdf Package: seqLogo Version: 1.2.0 Depends: methods, grid Title: Sequence logos for DNA sequence alignments Description: seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990). biocViews: SequenceMatching Author: Oliver Bembom Maintainer: Oliver Bembom License: LGPL version 2 or newer source.ver: src/contrib/seqLogo_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/seqLogo_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/seqLogo_1.2.0.tgz vignettes: vignettes/seqLogo/inst/doc/seqLogo.pdf Package: sigPathway Version: 1.4.0 Depends: R (>= 2.0.0) Suggests: hgu133a (>= 1.10.0) Title: Pathway Analysis Description: Conducts pathway analysis by calculating the NT_k and NE_k statistics as described in Tian et al. (2005) biocViews: Statistics, DifferentialExpression, MultipleComparisons Author: Weil Lai (optimized R and C code), Lu Tian and Peter Park (algorithm development and initial R code) Maintainer: Weil Lai URL: http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102, http://www.chip.org/~ppark/Supplements/PNAS05.html License: GPL 2 source.ver: src/contrib/sigPathway_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/sigPathway_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/sigPathway_1.4.0.tgz vignettes: vignettes/sigPathway/inst/doc/sigPathway-vignette.pdf Package: siggenes Version: 1.10.1 Depends: methods, multtest, Biobase, splines Suggests: affy, annotate, genefilter Title: SAM and Efron's empirical Bayes approaches Description: Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM). biocViews: DifferentialExpression, Microarray, SNPsAndGeneticVariability Author: Holger Schwender Maintainer: Holger Schwender License: Free for non-commercial use. Non-academic users MUST have a valid license for the full (Excel) version of the SAM software programmed at Stanford University, see http://www-stat.stanford.edu/~tibs/SAM/index.html source.ver: src/contrib/siggenes_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/siggenes_1.10.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/siggenes_1.10.1.tgz vignettes: vignettes/siggenes/inst/doc/siggenes.pdf Package: simpleaffy Version: 2.10.31 Depends: R (>= 2.0.0), affy, genefilter, Biobase, methods, utils Title: Very simple high level analysis of Affymetrix data Description: Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures... biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Transcription, DataImport, Statistics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Crispin J Miller Maintainer: Crispin Miller URL: http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/ License: GPL version 2 or later source.ver: src/contrib/simpleaffy_2.10.31.tar.gz win.binary.ver: bin/windows/contrib/2.5/simpleaffy_2.10.31.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/simpleaffy_2.10.31.tgz vignettes: vignettes/simpleaffy/inst/doc/QCandSimpleaffy.pdf, vignettes/simpleaffy/inst/doc/simpleAffy.pdf Package: simulatorAPMS Version: 1.8.0 Depends: graph, apComplex, Rgraphviz, ScISI, ppiStats Title: Computationally simulates the AP-MS technology. Description: Functions to computationally simulate the AP-MS technology based on wet-lab data. biocViews: MassSpectrometry, GraphsAndNetworks Author: Tony Chiang Maintainer: Tony Chiang License: LGPL source.ver: src/contrib/simulatorAPMS_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/simulatorAPMS_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/simulatorAPMS_1.8.0.tgz vignettes: vignettes/simulatorAPMS/inst/doc/simulatorAPMS.pdf Package: sizepower Version: 1.6.0 Depends: stats Title: Sample Size and Power Calculation in Micorarray Studies Description: This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice. biocViews: Microarray, Statistics Author: Weiliang Qiu and Mei-Ling Ting Lee and George Alex Whitmore Maintainer: Weiliang Qiu License: LGPL source.ver: src/contrib/sizepower_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/sizepower_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/sizepower_1.6.0.tgz vignettes: vignettes/sizepower/inst/doc/sizepower.pdf Package: snapCGH Version: 1.4.0 Depends: limma, tilingArray, DNAcopy, GLAD, cluster, methods, aCGH Title: Segmentation, normalisation and processing of aCGH data. Description: Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. biocViews: Microarray, DNACopyNumber, TwoChannel, Preprocessing Author: Mike L. Smith, John C. Marioni, Steven McKinney, Tom J. Hardcastle, Natalie P. Thorne Maintainer: John Marioni License: GPL source.ver: src/contrib/snapCGH_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/snapCGH_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/snapCGH_1.4.0.tgz vignettes: vignettes/snapCGH/inst/doc/snapCGHguide.pdf Package: spikeLI Version: 1.4.0 Depends: utils Title: Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool Description: SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006). biocViews: Microarray, QualityControl Author: Delphine Baillon, Paul Leclercq , Sarah Ternisien, Thomas Heim, Enrico Carlon Maintainer: Enrico Carlon License: Free Software Licence, GPL source.ver: src/contrib/spikeLI_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/spikeLI_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/spikeLI_1.4.0.tgz vignettes: vignettes/spikeLI/inst/doc/IvsDG_TagE.pdf, vignettes/spikeLI/inst/doc/Ivsc.pdf, vignettes/spikeLI/inst/doc/collapse_A14.pdf, vignettes/spikeLI/inst/doc/langmuir2.pdf, vignettes/spikeLI/inst/doc/spikeLI.pdf Package: splicegear Version: 1.8.0 Depends: R (>= 1.9.0), methods, utils, grid, Biobase(>= 1.3.24), XML (>= 0.92-2), annotate(>= 1.0.21) Title: splicegear Description: A set of tools to work with alternative splicing biocViews: Infrastructure, Transcription Author: Laurent Gautier Maintainer: Laurent License: LGPL source.ver: src/contrib/splicegear_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/splicegear_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/splicegear_1.8.0.tgz vignettes: vignettes/splicegear/inst/doc/splicegear.pdf Package: splots Version: 1.2.0 Depends: R (>= 2.3.0), grid Title: Visualization routines for high throughput screens Description: A stand alone collection of generic plot and visualization routines for high throuput screens and similar data of general formats. The emphasis is on having as few dependencies as possible to ensure interoperability! At the moment there is only one function, but functionality will be added as opportunity arises. Author: Oleg Sklyar Maintainer: Oleg Sklyar License: LGPL source.ver: src/contrib/splots_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/splots_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/splots_1.2.0.tgz vignettes: vignettes/splots/inst/doc/splotsHOWTO.pdf Package: spotSegmentation Version: 1.10.0 Depends: R (>= 1.7.0), mclust Title: Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots Description: Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington. biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Qunhua Li, Chris Fraley, Adrian Raftery Department of Statistics, University of Washington Maintainer: Chris Fraley URL: http://www.stat.washington.edu/fraley License: GPL version 2 or higher source.ver: src/contrib/spotSegmentation_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/spotSegmentation_1.10.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/spotSegmentation_1.10.0.tgz vignettes: vignettes/spotSegmentation/inst/doc/spotsegdoc.pdf Package: sscore Version: 1.8.0 Depends: R (>= 1.8.0), affy Title: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays Description: This package contains an implementation of the S-Score algorithm as described by Zhang et al (2002). biocViews: Statistics, DifferentialExpression Author: Richard Kennedy , based on C++ code from Li Zhang and Borland Delphi code from Robnet Kerns . Maintainer: Richard Kennedy URL: http://home.att.net/~richard-kennedy/professional.html License: GPL version 2 or newer source.ver: src/contrib/sscore_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/sscore_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/sscore_1.8.0.tgz vignettes: vignettes/sscore/inst/doc/sscore.pdf Package: ssize Version: 1.8.0 Depends: gdata, xtable Title: Estimate Microarry Sample Size Description: Functions for computing and displaying sample size information for gene expression arrays. biocViews: Statistics, Microarray, DifferentialExpression Author: Gregory R. Warnes, Peng Liu, and Fasheng Li Maintainer: Gregory R. Warnes License: LGPL source.ver: src/contrib/ssize_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/ssize_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/ssize_1.8.0.tgz vignettes: vignettes/ssize/inst/doc/ssize.pdf Package: stepNorm Version: 1.8.0 Depends: R (>= 1.8.0), marray, MASS, methods Title: Stepwise normalization functions for cDNA microarrays Description: Stepwise normalization functions for cDNA microarray data. biocViews: Microarray, TwoChannel, Preprocessing Author: Yuanyuan Xiao , Yee Hwa (Jean) Yang Maintainer: Yuanyuan Xiao URL: http://www.biostat.ucsf.edu/jean/ License: LGPL source.ver: src/contrib/stepNorm_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/stepNorm_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/stepNorm_1.8.0.tgz Package: tilingArray Version: 1.14.0 Depends: R (>= 2.5.0), methods, Biobase (>= 1.13.50), affy (>= 1.11.6), RColorBrewer (>= 0.2-3), grid (>= 2.0.0), strucchange (>= 1.3-0), vsn (>= 2.0.35), genefilter (>= 1.11.8), geneplotter (>= 1.11.9), pixmap (>= 0.4-4) Title: Analysis of high-density oligonucleotide tiling arrays Description: The package provides some functionalities that can be useful for the analysis of high-density tiling microarray data (such as Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: The class 'segmentation' for representing partitionings of a linear series of data. The functions 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact, and 'confint' for calculating confidence intervals using the strucchange package. The function 'plotAlongChrom' for generating pretty plots. The function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations. biocViews: Microarray, OneChannel, Preprocessing, Visualization Author: Wolfgang Huber, Joern Toedling, Matt Ritchie Maintainer: W. Huber License: The Artistic License, Version 2.0 source.ver: src/contrib/tilingArray_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/tilingArray_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/tilingArray_1.14.0.tgz vignettes: vignettes/tilingArray/inst/doc/assessNorm.pdf, vignettes/tilingArray/inst/doc/costMatrix.pdf, vignettes/tilingArray/inst/doc/findsegments.pdf, vignettes/tilingArray/inst/doc/segmentation.pdf Package: tkWidgets Version: 1.14.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0) Suggests: Biobase Title: R based tk widgets Description: Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. biocViews: Infrastructure Author: J. Zhang Maintainer: J. Zhang License: LGPL source.ver: src/contrib/tkWidgets_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/tkWidgets_1.14.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/tkWidgets_1.14.0.tgz vignettes: vignettes/tkWidgets/inst/doc/importWizard.pdf, vignettes/tkWidgets/inst/doc/tkWidgets.pdf Package: topGO Version: 1.2.1 Depends: R (>= 2.4.0), methods, graph (>= 1.14.0), Biobase (>= 1.14.0), GO (>= 1.14.0), annotate (>= 1.14.0), SparseM (>= 0.73) Imports: methods, graph (>= 1.14.0), Biobase (>= 1.14.0), SparseM (>= 0.73), annotate (>= 1.14.0) Suggests: ALL, hgu95av2, genefilter, xtable, multtest, Rgraphviz, hgu133a Title: topGO: Enrichment analysis for Gene Ontology Description: topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. biocViews: Microarray,Statistics,Visualization Author: Adrian Alexa, Jorg Rahnenfuhrer Maintainer: Adrian Alexa License: LGPL source.ver: src/contrib/topGO_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.5/topGO_1.2.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/topGO_1.2.1.tgz vignettes: vignettes/topGO/inst/doc/topGO.pdf Package: twilight Version: 1.12.0 Depends: R (>= 2.1.0), splines (>= 2.2.0), stats (>= 2.2.0),Biobase(>= 1.12.0) Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) Title: Estimation of local false discovery rate Description: In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package TWILIGHT contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. biocViews: Microarray, Statistics, DifferentialExpression, MultipleComparisons Author: Stefanie Scheid Maintainer: Stefanie Scheid URL: http://compdiag.molgen.mpg.de/software/twilight.shtml License: GPL version 2.0 or newer source.ver: src/contrib/twilight_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/twilight_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/twilight_1.12.0.tgz vignettes: vignettes/twilight/inst/doc/bcb_logo.pdf, vignettes/twilight/inst/doc/tr_2004_01.pdf Package: vsn Version: 2.2.0 Depends: R (>= 2.5.0), Biobase (>= 1.4.14), methods, affy, limma Suggests: affydata, hgu95av2cdf, geneplotter Title: Variance stabilization and calibration for microarray data Description: The package implements a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (aka normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. biocViews: Microarray, OneChannel, TwoChannel, Preprocessing Author: Wolfgang Huber , contributions from A. von Heydebreck , Markus Ruschhaupt , D. Kostka Maintainer: Wolfgang Huber URL: http://www.r-project.org, http://www.ebi.ac.uk/huber License: Artistic License 2.0 source.ver: src/contrib/vsn_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/vsn_2.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/vsn_2.2.0.tgz vignettes: vignettes/vsn/inst/doc/convergence2.pdf, vignettes/vsn/inst/doc/incremental.pdf, vignettes/vsn/inst/doc/vsn.pdf Package: weaver Version: 1.2.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools Title: Tools and extensions for processing Sweave documents Description: This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included. biocViews: Infrastructure Author: Seth Falcon Maintainer: Seth Falcon License: GPL2 source.ver: src/contrib/weaver_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/weaver_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/weaver_1.2.0.tgz vignettes: vignettes/weaver/inst/doc/weaver_howTo.pdf Package: webbioc Version: 1.8.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Title: Bioconductor Web Interface 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.) biocViews: Infrastructure, Microarray, OneChannel, DifferentialExpression Author: Colin A. Smith Maintainer: Colin A. Smith URL: http://www.bioconductor.org/ License: GPL version 2 or newer SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm source.ver: src/contrib/webbioc_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/webbioc_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/webbioc_1.8.0.tgz vignettes: vignettes/webbioc/inst/doc/demoscript.pdf, vignettes/webbioc/inst/doc/webbioc.pdf Package: widgetTools Version: 1.12.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase Title: Creates an interactive tcltk widget Description: This packages contains tools to support the construction of tcltk widgets biocViews: Infrastructure Author: Jianhua Zhang Maintainer: Jianhua Zhang License: LGPL source.ver: src/contrib/widgetTools_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/widgetTools_1.12.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/widgetTools_1.12.0.tgz vignettes: vignettes/widgetTools/inst/doc/widget.pdf, vignettes/widgetTools/inst/doc/widgetTools.pdf Package: xcms Version: 1.8.0 Depends: R (>= 1.9.0), methods Suggests: faahKO, multtest, rgl Title: LC/MS and GC/MS Data Analysis Description: Framework for processing and visualization of chromatographically separated mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling. biocViews: Technology,MassSpectrometry Author: Colin A. Smith , Ralf Tautenhahn Maintainer: Colin A. Smith URL: http://metlin.scripps.edu/download/ License: GPL version 2 or newer SystemRequirements: NetCDF, zlib source.ver: src/contrib/xcms_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.5/xcms_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.5/xcms_1.8.0.tgz vignettes: vignettes/xcms/inst/doc/FlowChart.pdf, vignettes/xcms/inst/doc/xcmsInstall.pdf, vignettes/xcms/inst/doc/xcmsPreprocess.pdf