PGPC
This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see PGPC.
Experimental data and analysis of the chemical-genetic interaction screen in isogenic HCT116 cell lines
Bioconductor version: 3.7
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("PGPC")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PGPC")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PGPC")| PGPC | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CancerData, ColonCancerData, ExperimentData |
| Version | 1.8.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.0), EBImage, imageHTS, SearchTrees, limma, RColorBrewer, gplots, splots, ggplot2, geneplotter, ChemmineR, reshape2, plyr |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PGPC_1.8.0.tar.gz |
| 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 | https://bioconductor.org/packages/PGPC/ |
| Package Downloads Report | Download Stats |