Package: idiogram
Version: 1.48.0
Title: idiogram
Description: A package for plotting genomic data by chromosomal location
Author: Karl J. Dykema <karl.dykema@vai.org>
Maintainer: Karl J. Dykema <karl.dykema@vai.org>
Depends: R (>= 2.10), methods, Biobase, annotate, plotrix
Suggests: hu6800.db, hgu95av2.db, golubEsets
License: GPL-2
ZipData: no
biocViews: Visualization
LazyData: yes
NeedsCompilation: no
Packaged: 2016-05-04 02:44:55 UTC; biocbuild
Package: macat
Title: MicroArray Chromosome Analysis Tool
Version: 1.46.0
Date: 2014-01-15
Author: Benjamin Georgi, Matthias Heinig, Stefan Roepcke, Sebastian
Schmeier, Joern Toedling
Depends: Biobase, annotate
Suggests: hgu95av2.db, stjudem
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'.
Maintainer: Joern Toedling <jtoedling@yahoo.de>
License: Artistic-2.0
biocViews: Microarray, DifferentialExpression, Visualization
Reference: Toedling J, Schmeier S, Heinig M, Georgi B, Roepcke S
(2005). MACAT - MicroArray Chromosome Analysis Tool.
Bioinformatics. 21(9):2112--2113.
NeedsCompilation: no
Packaged: 2016-05-04 02:43:27 UTC; biocbuild
Package: phenoTest
Type: Package
Title: Tools to test association between gene expression and phenotype
in a way that is efficient, structured, fast and scalable. We
also provide tools to do GSEA (Gene set enrichment analysis)
and copy number variation.
Version: 1.20.0
Date: 2013-05-29
Author: Evarist Planet
Maintainer: Evarist Planet <evarist.planet@epfl.ch>
Description: Tools to test correlation between gene expression and
phenotype in a way that is efficient, structured, fast and
scalable. GSEA is also provided.
License: GPL (>=2)
Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2
Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR, ellipse
Suggests: GSEABase, KEGG.db, GO.db
Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
LazyLoad: yes
biocViews: Microarray, DifferentialExpression, MultipleComparison,
Clustering, Classification
NeedsCompilation: no
Packaged: 2016-05-04 03:54:59 UTC; biocbuild
Package: GeneAnswers
Type: Package
Title: Integrated Interpretation of Genes
Version: 2.14.0
Date: 2014-10-1
Depends: R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer
Imports: RBGL, annotate, downloader
Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph
Author: Lei Huang, Gang Feng, Pan Du, Tian Xia, Xishu Wang, Jing, Wen, Warren Kibbe and Simon Lin
Maintainer: Lei Huang <lhuang7@uchicago.edu> and Gang Feng <gilbertfeng@gmail.com>
Description: GeneAnswers provides an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test.
License: LGPL (>= 2)
biocViews: Infrastructure, DataRepresentation, Visualization,
GraphsAndNetworks
LazyLoad: yes
Packaged: 2016-05-04 03:22:43 UTC; biocbuild
NeedsCompilation: no
Package: ChromHeatMap
Version: 1.26.0
Date: 2009-10-06
Title: Heat map plotting by genome coordinate
Description: The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.
Author: Tim F. Rayner
Maintainer: Tim F. Rayner <tfrayner@gmail.com>
Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0)
Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer
Suggests: ALL, hgu95av2.db
License: Artistic-2.0
biocViews: Visualization
NeedsCompilation: no
Packaged: 2016-05-04 03:19:37 UTC; biocbuild
Package: RpsiXML
Version: 2.14.0
Date: 2015-04-09
Title: R interface to PSI-MI 2.5 files
Author: Jitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2), AnnotationDbi
Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, Rgraphviz, ppiStats, ScISI
Description: Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.
Collate: AllClasses.R AllGenerics.R AllMethods.R SAXhandlers.R
funcsAnnotation.R hyperGraphs.R psi25parser.R psimi25Source.R
validatePSIMI25.R graphSpeciesConverter.R
License: LGPL-3
URL: http://www.bioconductor.org
biocViews: Infrastructure, Proteomics
NeedsCompilation: no
Packaged: 2016-05-04 03:09:44 UTC; biocbuild
Package: Neve2006
Title: expression and CGH data on breast cancer cell lines
Version: 0.10.0
Author: M. Neve et al. in Gray Lab at LBL
Description: Experimental organization of combined expression and CGH data
Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
LazyLoad: yes
biocViews: ExperimentData, CancerData, BreastCancerData
Packaged: 2016-05-07 20:12:57 UTC; biocbuild
NeedsCompilation: no
Package: PCpheno
Type: Package
Title: Phenotypes and cellular organizational units
Version: 1.34.0
Author: Nolwenn Le Meur and Robert Gentleman
Description: Tools to integrate, annotate, and link phenotypes to
cellular organizational units such as protein complexes and
pathways.
Depends: R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats, ppiData, annotate (>= 1.17.4)
Imports: AnnotationDbi, Biobase, Category, GO.db, graph, graphics, GSEABase, KEGG.db, methods, ScISI, stats, stats4
Suggests: KEGG.db, GO.db, org.Sc.sgd.db
Maintainer: Nolwenn Le Meur <nlemeur@gmail.com>
License: Artistic-2.0
biocViews: GraphAndNetwork, Proteomics, Network
NeedsCompilation: no
Packaged: 2016-05-04 03:05:41 UTC; biocbuild
Package: PREDAsampledata
Title: expression and copy number data on clear cell renal carcinoma
samples
Version: 0.12.0
Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan
Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0)
Depends: R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate, gahgu133plus2.db, gahgu133plus2cdf
Suggests: hgu133plus2.db, hgu133plus2cdf
Maintainer: Francesco Ferrari <francesco.ferrari@unimore.it>
License: Artistic-2.0
biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData,
MicroarrayData, TissueMicroarrayData, ArrayExpress
NeedsCompilation: no
Packaged: 2016-05-07 20:19:54 UTC; biocbuild
providing 
.