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 (3.17)

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 "4.3") and enter:

if (!require("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

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

Details

biocViews CellBasedAssays, Cheminformatics, CopyNumberVariation, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software, SystemsBiology, Visualization, aCGH, miRNA
Version 2.21.0
In Bioconductor since BioC 3.1 (R-3.2) (7.5 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, 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_2.21.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
Package Downloads Report Download Stats

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