rcellminer

DOI: 10.18129/B9.bioc.rcellminer  

rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

Bioconductor version: Release (3.16)

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa

Maintainer: Augustin Luna <lunaa at cbio.mskcc.org>, Vinodh Rajapakse <vinodh.rajapakse at nih.gov>, Fathi Elloumi <fathi.elloumi at nih.gov>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rcellminer")

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("rcellminer")

 

HTML	R Script	Using rcellminer
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, Cheminformatics, CopyNumberVariation, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software, SystemsBiology, Visualization, aCGH, miRNA
Version	2.20.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 years)
License	LGPL-3 + file LICENSE
Depends	R (>= 3.2), Biobase, rcellminerData(>= 2.0.0)
Imports	stringr, gplots, ggplot2, methods, stats, utils, shiny
LinkingTo
Suggests	knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown
SystemRequirements
Enhances
URL	http://discover.nci.nih.gov/cellminer/
Depends On Me
Imports Me
Suggests Me	rcellminerData
Links To Me
Build Report

Package Archives

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

Source Package	rcellminer_2.20.0.tar.gz
Windows Binary	rcellminer_2.20.0.zip
macOS Binary (x86_64)	rcellminer_2.20.0.tgz
macOS Binary (arm64)	rcellminer_2.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rcellminer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rcellminer
Bioc Package Browser	https://code.bioconductor.org/browse/rcellminer/
Package Short Url	https://bioconductor.org/packages/rcellminer/
Package Downloads Report	Download Stats