rcellminer
This is the released version of rcellminer; for the devel version, see rcellminer.
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
Bioconductor version: Release (3.23)
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 <augustin.luna at nih.gov>, Vinodh Rajapakse <vinodh.rajapakse at nih.gov>, Fathi Elloumi <fathi.elloumi at nih.gov>
citation("rcellminer")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Using rcellminer | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, Cheminformatics, CopyNumberVariation, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software, SystemsBiology, Visualization, aCGH, miRNA |
| Version | 2.34.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | LGPL-3 + file LICENSE |
| Depends | R (>= 3.2), Biobase, rcellminerData(>= 2.0.0) |
| Imports | stringr, gplots, ggplot2, methods, stats, utils, shiny |
| System Requirements | |
| URL | http://discover.nci.nih.gov/cellminer/ |
See More
| Suggests | knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | rcellminerData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rcellminer_2.34.0.tar.gz |
| Windows Binary (x86_64) | rcellminer_2.34.0.zip |
| macOS Binary (big-sur-x86_64) | rcellminer_2.34.0.tgz |
| macOS Binary (sonoma-arm64) | rcellminer_2.34.0.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 |