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Bioinformatics. 2016 Apr 15;32(8):1272-4. doi: 10.1093/bioinformatics/btv701. Epub 2015 Dec 3.

rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R.

Author information

1
Computer Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA.
2
Developmental Therapeutic Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
3
Centro De Estudos Em Células Tronco, Terapia Celular E Genética Toxicológica, Programa De Pós-Graduação Em Farmácia, Universidade Federal De Mato Grosso Do Sul, Campo Grande, MS 79070-900, Brazil and.
4
Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA.

Abstract

PURPOSE:

The rcellminer R package provides a wide range of functionality to help R users access and explore molecular profiling and drug response data for the NCI-60. The package enables flexible programmatic access to CellMiner's unparalleled breadth of NCI-60 data, including gene and protein expression, copy number, whole exome mutations, as well as activity data for ∼21K compounds, with information on their structure, mechanism of action and repeat screens. Functions are available to easily visualize compound structures, activity patterns and molecular feature profiles. Additionally, embedded R Shiny applications allow interactive data exploration.

AVAILABILITY AND IMPLEMENTATION:

rcellminer is compatible with R 3.2 and above on Windows, Mac OS X and Linux. The package, documentation, tutorials and Shiny-based applications are available through Bioconductor (http://www.bioconductor.org/packages/rcellminer); ongoing updates will occur according to the Bioconductor release schedule with new CellMiner data. The package is free and open-source (LGPL 3).

CONTACT:

lunaa@cbio.mskcc.org or vinodh.rajapakse@nih.gov.

PMID:
26635141
PMCID:
PMC4907377
DOI:
10.1093/bioinformatics/btv701
[Indexed for MEDLINE]
Free PMC Article

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