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Update RegulomeExplorerNotebooks.rst
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DeenaBleich committed Jun 15, 2023
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Expand Up @@ -58,4 +58,4 @@ Regulome Explorer Inspired Notebook
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`Regulome Explorer <http://explorer.cancerregulome.org/>`_ is a well-established web tool for the exploration and visualization of associations between clinical and molecular features of TCGA data. Regulome Explorer was developed in 2012 in close collaboration between the Institute for Systems Biology and the MD Anderson Cancer Center. It enables users to search and visualize precomputed statistical data filtered according to user-specified parameters. Although Regulome Explorer's broad functionality and high-quality graphics make it a valuable tool for exploring and visualizing 20 of the 33 TCGA data sets, it does not yet contain analysis of recent releases of TCGA and cannot be easily applied to data sets other than TCGA.

We developed a more flexible version, replicating capabilities of Regulome Explorer, as a Python notebook that uses Google Cloud resources. Rather than working with precomputed, fixed cohorts and fixed results, statistical analyses are dynamically performed in the cloud, with user defined patient cohorts. Moreover, the notebook can be extended so that users can analyze additional data sets available as part of the 'ISB-CGC BigQuery ecosystem' such as TCGA, TARGET, CCLE, COSMIC, and others. The notebook can be accessed in `Regulome Explorer inspired notebook <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/RegulomeExplorer/RegulomeExplorer-notebook.ipynb>`_.
We developed a more flexible version, replicating capabilities of Regulome Explorer, as a Python notebook that uses Google Cloud resources. Rather than working with precomputed, fixed cohorts and fixed results, statistical analyses are dynamically performed in the cloud, with user defined patient cohorts. Moreover, the notebook can be extended so that users can analyze additional data sets available as part of the 'ISB-CGC BigQuery ecosystem' such as TCGA, TARGET, CCLE, and others. The notebook can be accessed in `Regulome Explorer inspired notebook <https://nbviewer.jupyter.org/github/isb-cgc/Community-Notebooks/blob/master/RegulomeExplorer/RegulomeExplorer-notebook.ipynb>`_.

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