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: HMMcopy
Type: Package
Title: Copy number prediction with correction for GC and mappability
bias for HTS data
Version: 1.14.0
Date: 2012-08-27
Author: Daniel Lai, Gavin Ha, Sohrab Shah
Maintainer: Daniel Lai <jujubix@cs.ubc.ca>, Gavin Ha <gha@bccrc.ca>,
Sohrab Shah <sshah@bccrc.ca>
Import: IRanges
Depends: R (>= 2.10.0), IRanges (>= 1.4.16), geneplotter (>= 1.24.0)
Description: Corrects GC and mappability biases for readcounts (i.e.
coverage) in non-overlapping windows of fixed length for single
whole genome samples, yielding a rough estimate of copy number
for furthur analysis. Designed for rapid correction of high
coverage whole genome tumour and normal samples.
License: GPL-3
biocViews: Sequencing, Preprocessing, Visualization,
CopyNumberVariation, Microarray
NeedsCompilation: yes
Packaged: 2016-05-04 04:44:45 UTC; biocbuild
Package: Hiiragi2013
Type: Package
Title: Cell-to-cell expression variability followed by signal
reinforcement progressively segregates early mouse lineages
Version: 1.8.0
Author: Andrzej Oles, Wolfgang Huber
Maintainer: Andrzej Oles <andrzej.oles@embl.de>
Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881."
License: Artistic-2.0
LazyLoad: true
Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable
Imports: grid, lattice, latticeExtra
Suggests: ArrayExpress, BiocStyle
biocViews: ExperimentData, MicroarrayData, qPCRData,
ReproducibleResearch
NeedsCompilation: no
Packaged: 2016-05-07 20:43:09 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