PGPC

DOI: 10.18129/B9.bioc.PGPC    

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

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PGPC")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("PGPC")

 

PDF	R Script	PGPC
PDF		Reference Manual
Text		NEWS

Details

biocViews	CancerData, ColonCancerData, ExperimentData
Version	1.6.0
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
Build Report

Package Archives

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

Source Package	PGPC_1.6.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/PGPC
Package Short Url	http://bioconductor.org/packages/PGPC/
Package Downloads Report	Download Stats