Package: HD2013SGI
Type: Package
Title: Mapping genetic interactions in human cancer cells with RNAi and
multiparametric phenotyping
Version: 1.12.0
Author: Bernd Fischer
Maintainer: Bernd Fischer <b.fischer@dkfz.de>
Description: This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.
License: Artistic-2.0
LazyLoad: true
Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD, EBImage
Suggests: BiocStyle
SystemRequirements: GNU make
biocViews: ExperimentData, CancerData, ColonCancerData,
MicrotitrePlateAssayData, CellCulture, Homo_sapiens_Data,
HighThroughputImagingData
NeedsCompilation: no
Packaged: 2016-05-07 20:40:24 UTC; biocbuild
Package: PGPC
Type: Package
Title: Experimental data and analysis of the chemical-genetic
interaction screen in isogenic HCT116 cell lines
Version: 1.0.2
Author: Felix Klein
Maintainer: Felix Klein <felix.klein@embl.de>
Description: This package contains the experimental data and a vignette
guiding through the analysis of a chemical-genenetic
interaction screen in isogenic HCT116 cell lines. The code can
be executed to generate all results and figures for the
manuscript "A chemical-genetic interaction map of small molecules using
high-throughput imaging in cancer cells" accepted for publicaton at
Molecular Systems Biology. Data availability: Complementary views on
this dataset are available through different repositories. The image
data files are available from the BioStudies database at the European
Bioinformatics Institute (EMBL-EBI) under the accession S-BSMS-PGPC1
(http://wwwdev.ebi.ac.uk/biostudies/studies/S-BSMS-PGPC1)
An interactive front-end for exploration of the images is provided by
the IDR database http://dx.doi.org/10.17867/10000101.
The authors are hosting an interactive webpage to browse images and
interaction profiles at http://dedomena.embl.de/PGPC.
License: Artistic-2.0
LazyLoad: true
Depends: R (>= 3.0), EBImage, imageHTS, SearchTrees, limma, RColorBrewer, gplots, splots, ggplot2, geneplotter, ChemmineR, reshape2, plyr
VignetteBuilder: knitr
Suggests: BiocStyle, knitr
biocViews: CancerData, ColonCancerData, ExperimentData
NeedsCompilation: no
Packaged: 2016-05-28 15:50:08 UTC; biocbuild
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
providing 
.