Package: AccuPloidy Version: 2.12.1 Depends: R (>= 2.11), methods License: Artistic-2.0 Title: Classes and methods for estimating ploidy from SNP chips Description: This package defines the classes used to estimate ploidy in order to renormalize SNP chip data for accurate copy number estimation. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2009-12-01 MD5sum: 7f78db70baaf2353a30b3a7d1312c253 Package: ArrayCube Version: 0.6.1 Depends: R (>= 2.11), methods, XML, Biobase, oompaBase, PreProcess Suggests: limma License: Artistic-2.0 Title: Data structures for raw spotted array data Description: This package defines data structures and import functions for raw data from spotted microarrays. The structures are similar to the ExpressionSet class. The structure allows for the addition of import functions for new quantification software without having to touch existing code. ArrayCubes can easily be converted to the structures used by limma or marray. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-22 MD5sum: 5d8beb276e9cdc64cbe93284b9d4d0d1 Package: CRAAC Version: 1.0.2 Depends: R (>= 2.10), methods, cluster, mclust, ClassDiscovery Suggests: Biobase License: Artistic-2.0 Title: Classes and methods for consistent, algorithm-agnostic, robust clustering Description: This package extends the classes used for "class discovery" problems in the OOMPA project. Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2011-12-01 MD5sum: f3181da1df427975d283446253f63b69 Package: ClassComparison Version: 2.15.0 Depends: R (>= 2.10), methods, splines, Biobase, oompaBase (>= 2.10), PreProcess (>= 2.10) License: Artistic-2.0 Title: Classes and methods for "class comparison" problems on microarrays Description: This package defines the classes used for "class comparison" problems in the OOMPA project. Class comparison includes tests for differential expression; see Simon's book for details on typical problem types. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-01 MD5sum: 50824d36b5d9f357c8899350c5eb07d6 Package: ClassDiscovery Version: 2.13.4 Depends: R (>= 2.10), methods, stats, cluster, mclust, oompaBase (>= 2.10), PreProcess (>= 2.10) Suggests: Biobase, xtable License: Artistic-2.0 Title: Classes and methods for "class discovery" with microarrays or proteomics Description: This package defines the classes used for "class discovery" problems in the OOMPA project. Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-01 MD5sum: 0759d4d7712771b0b4850b6e34454bd9 Package: ClassPrediction Version: 2.10.2 Depends: R (>= 2.10), GenAlgo (>= 1.0), CrossVal (>= 1.0) Suggests: Biobase License: Artistic-2.0 Title: Classes and methods for "class prediction" with microarrays or proteomics Description: This package bundles the classes and pacakges used to help with "class prediction" problems in the OOMPA project. Class prediction consists of supervised methods to select relevant features and construct predictive models for binary, ordinal, continuous, or survival outcomes. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-01 MD5sum: ca805d1c232822c858a2086ff16dc909 Package: CrossVal Version: 1.0.1 Depends: R (>= 2.10), methods, PreProcess (>= 2.10), ClassComparison, ClassDiscovery, rpart, TailRank, class Suggests: Biobase License: Artistic-2.0 Title: Classes and methods for cross validation of "class prediction" with microarrays or proteomics Description: This package defines classes and methods to cross validate methods for "class prediction". These are generic tools, but also include specific examples for some common classifiers. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-04 MD5sum: 5b3a78ae2bebc5ba46ec7d46f56214ef Package: FirstSign Version: 0.1.0 Depends: R (>= 2.10), ClassDiscovery, methods, stats License: Artistic-2.0 Title: FirstSign Package Description: FirstSign is a package that turns gene signatures (in their primitive form as simply a list of gene names) into actual predictors, by using the first principal component. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2013-03-27 MD5sum: 16cb501970b6df097e388b7f3e58b9ab Package: GenAlgo Version: 1.0.3 Depends: R (>= 2.10), methods, MASS, oompaBase (>= 2.10), PreProcess (>= 2.10), ClassDiscovery Suggests: Biobase, xtable License: Artistic-2.0 Title: Classes and methods to use genetic algorithms for feature selection Description: This package defines classes and methods that can be used to implement genetic algorithms for feature selection. The idea is that we want to select a fixed number of features to combine into a linear classifier that can predict a binary outcome, and can use a genetic algorithm heuristically to select an optimal set of features. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-07-01 MD5sum: 67fd8945878a9d5dd605dd2fefb77cc2 Package: MINiML Version: 0.6.1 Depends: R (>= 2.4), methods, XML, Biobase, PreProcess, ArrayCube, limma License: Artistic-2.0 Title: Package for reading data from GEO in MINiML format Description: This package defines import functions for raw data in MINiML format. Data is read into an ArrayCube, which can then be converted to an AffyBatch or an RGLIst as appropriate. The package includes a data set in MINiML format. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-01 MD5sum: 059e7d9339be89070c82ee652f748c6a Package: NameNeedle Version: 1.1.1 Depends: R (>= 2.10), stats License: GPL (>= 2) Title: NameNeedle package Description: Using Needleman-Wunsch to Match Sample Names Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-01 MD5sum: cc243d85da76a221eb157ebdb745a3a3 Package: PreProcess Version: 2.12.2 Depends: R (>= 2.10), methods, graphics, oompaBase (>= 2.10) License: Artistic-2.0 Title: Basic functions for microarray pre-processing Description: This package defines the basic classes used for the OOMPA (object-oriented microarray and proteomics analysis) project. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-01 MD5sum: d83f4842228e286819b8ba64d3d55e69 Package: SIBER Version: 0.9.2 Depends: mclust Suggests: edgeR,doSNOW License: GPL (>= 2) Title: Systematic Identification of Bimodally Expressed Genes Using RNAseq Data Description: SIBER(Systematic Identification of Bimodally Expressed genes using RNAseq data) effectively identifies bimodally expressed genes from RNAseq data based on Bimodality Index. SIBER models the RNAseq data in the finite mixture modeling framework and incorporates mechanisms for dealing with RNAseq normalization. Three types of mixture models are implemented, namely, the mixture of log normal, negative binomial, or generalized poisson distribution. Maintainer: Pan Tong Author: Pan Tong, Kevin R Coombes MD5sum: dc640c9fc0684406349c1c6d27c1fb17 Package: SlideDesignerGUI Version: 1.4.0 Depends: R (>= 2.11), tcltk, tclish (>= 0.8.2) License: Artistic-2.0 Title: Slide Designer GUI package Description: Graphical User Interface for recording layout of a slide design. Maintainer: P. Roebuck Author: P. Roebuck, based on earlier work by Kevin R. Coombes Date: 2011/04/01 MD5sum: 03131cf72d5540a1727b7f26fd3da1df Package: SuperCurveGUI Version: 2.0.1 Depends: R (>= 2.11), methods, tcltk, SuperCurve (>= 1.4), tclish (>= 0.8.2) License: Artistic-2.0 Title: SuperCurve GUI Package Description: Graphical User Interface for RPPA analysis using the SuperCurve package. Maintainer: P. Roebuck Author: P. Roebuck Date: 2011/05/20 MD5sum: 06a916e8058ee9f0cd616320733ad826 Package: SuperCurve Version: 1.4.4 Depends: R (>= 2.9), methods, stats, utils, graphics, grDevices, MASS, cobs Suggests: boot, mgcv, quantreg, robustbase, splines, timeDate License: Artistic-2.0 Title: SuperCurve Package Description: A package to analyze reverse phase protein lysate arrays. Maintainer: P. Roebuck Author: Kevin R. Coombes, Shannon Neeley, Corwin Joy, Jianhua Hu, Keith Baggerly, and P. Roebuck. Date: 2012/05/01 MD5sum: a58170b467e1d8b8fa8d33c8f0bb159c Package: TailRank Version: 2.11.0 Depends: R (>= 2.11), methods, stats, Biobase, oompaBase (>= 2.11), PreProcess (>= 2.11) License: GPL (>= 2) Title: The Tail-Rank Statistic Description: Implements the tail-rank statistic for selecting biomarkers from a microarray data set, an efficient nonparametric test focused on the distributional tails. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2011-12-01 MD5sum: e07225f600c6a6f5f74dfe7f11c4202c Package: Umpire Version: 1.2.4 Depends: R (>= 2.10), methods, stats Suggests: mclust, survival License: Artistic-2.0 Title: Umpire Package Description: The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray dataset. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes, Jiexin Zhang Date: 2012-06-01 MD5sum: 1a05c19beb315321e0c1b0d3b420e771 Package: estimate Version: 1.0.6 Depends: R (>= 2.15.1) Title: ESTIMATE: Estimate of STromal and Immune cells in MAlignant Tumor tissues using Expression data Description: A package for predicting tumor purity, and the presence of stromal/immune cells in tumor tissues using gene expression data. Maintainer: Kosuke Yoshihara Author: Kosuke Yoshihara, Hoon Kim, Roel GW Verhaak Date: 2013-05-21 MD5sum: 20d5dd48c9f871006e9f0c72c5d5350d Package: integIRTy Version: 0.9.4 Depends: ltm, foreach, doSNOW, mclust, MASS, abind License: GPL (>= 2) Title: Integrating Multiple Modalities of High Throughput Assays Using Item Response Theory Description: This package provides a systematic framework for integrating multiple modalities of assays profiled on the same set of samples. The goal is to identify genes that are altered in cancer either marginally or consistently across different assays. The heterogeneity among different platforms and different samples are automatically adjusted so that the overall alteration magnitude can be accurately inferred. Maintainer: Pan Tong Author: Pan Tong, Kevin R Coombes Date: 2012-06-04 MD5sum: aab388f248cbd36cc8d97a4523b99137 Package: oompaBase Version: 2.15.0 Depends: R (>= 2.15), methods License: Artistic-2.0 Title: Class unions and matrix operations for OOMPA Description: This package defines the class unions that must be preloaded in order for the basic tools in the OOMPA (object-oriented microarray and proteomics analysis) project to be defined and loaded. It also includes vectorized operations for row-by-row means, variances, and t-tests. Finally, it provides new color schemes. Maintainer: Kevin R. Coombes Author: Kevin R. Coombes Date: 2012-05-01 MD5sum: 78e1fe24cb6941966984d502ebeda34b Package: tclish Version: 0.8.3 Depends: R (>= 2.8), tcltk License: Artistic-2.0 Title: Tcl/Tk Utilities Package Description: Variety of Tcl/Tk methods used for GUI development. Maintainer: P. Roebuck Author: P. Roebuck Date: 2011/11/20 MD5sum: 4cd811c85de46dfe830458a1dbac6954