rcellminer

DOI: 10.18129/B9.bioc.rcellminer    

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

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

Bioconductor version: Development (3.13)

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>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("rcellminer")

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

Documentation

PDF   Reference Manual

Details

biocViews CellBasedAssays, Cheminformatics, CopyNumberVariation, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software, SystemsBiology, Visualization, aCGH, miRNA
Version 2.13.0
In Bioconductor since BioC 3.1 (R-3.2) (5.5 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, d3heatmap, glmnet, foreach, doSNOW, parallel
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
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/rcellminer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rcellminer
Package Short Url https://bioconductor.org/packages/rcellminer/
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