PGPC

DOI: 10.18129/B9.bioc.PGPC    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of PGPC; for the stable release version, see PGPC.

Experimental data and analysis of the chemical-genetic interaction screen in isogenic HCT116 cell lines

Bioconductor version: Development (3.9)

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.

Author: Felix Klein

Maintainer: Felix Klein <daggoth at gmx.de>

Citation (from within R, enter citation("PGPC")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("PGPC", version = "3.9")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews CancerData, ColonCancerData, ExperimentData
Version 1.11.2
License Artistic-2.0
Depends R (>= 3.0), EBImage, imageHTS, SearchTrees, limma, RColorBrewer, gplots, splots, ggplot2, geneplotter, ChemmineR, reshape2, plyr
Imports
LinkingTo
Suggests BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/PGPC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PGPC
Package Short Url http://bioconductor.org/packages/PGPC/
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