Augustin Luna1, Vinodh N Rajapakse2, Fabricio G Sousa3, Jianjiong Gao4, Nikolaus Schultz4, Sudhir Varma2, William Reinhold2, Chris Sander1, Yves Pommier2. 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. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.
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. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.
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