cellHTS2

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

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'cellHTS2' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'lines' from package 'graphics' in package 'cellHTS2'
** help
*** installing help indices
  converting help for package 'cellHTS2'
    finding HTML links ... done
    Bscore                                  html  
    Data                                    html  
    ROC-class                               html  
    ROC                                     html  
    annotate                                html  
    batch                                   html  
    bdgpbiomart                             html  
    buildCellHTS2                           html  
    cellHTS-class                           html  
    cellHTS2                                html  
    configurationAsScreenPlot               html  
    configure                               html  
    convertOldCellHTS                       html  
    convertWellCoordinates                  html  
    data-KcViab                             html  
    data-KcViabSmall                        html  
    data-dualCh                             html  
    data-oldKcViabSmall                     html  
    getDynamicRange                         html  
    getEnVisionRawData                      html  
    getMeasureRepAgreement                  html  
    getTopTable                             html  
    getZfactor                              html  
    gseaModule                              html  
    imageScreen                             html  
    intensityFiles                          html  
    normalizePlates                         html  
    oneRowPerId                             html  
    plate                                   html  
    plateEffects                            html  
    plotSpatialEffects                      html  
    readHTAnalystData                       html  
    readPlateList                           html  
    rsa                                     html  
    scoreReplicates                         html  
    scores2calls                            html  
    setSettings                             html  
    spatialNormalization                    html  
    state                                   html  
    summarizeChannels                       html  
    summarizeReplicates                     html  
    templateDescriptionFile                 html  
    updateCellHTS                           html  
    wellAnno                                html  
    write.tabdel                            html  
    writeReport                             html  
    writeTab                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cellHTS2)
Making 'packages.html' ... done