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smrgit committed Dec 29, 2015
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Expand Up @@ -71,12 +71,13 @@ TCGA Data Reports
A number of useful `Data Reports <https://tcga-data.nci.nih.gov/datareports/dataReportsHome.htm>`_
are available directly from TCGA. In particular:

* **`Data Statistics Dashboard <https://tcga-data.nci.nih.gov/datareports/statsDashboard.htm>`_** provides high-level statistics describing TCGA data content and use.
* **Data Statistics Dashboard**: provides high-level statistics describing
`TCGA data content and use <https://tcga-data.nci.nih.gov/datareports/statsDashboard.htm>`_.

Understanding Data Access
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* **Public Data** Sometimes the word "public" is misinterpreted as meaning "open". All of the TCGA data is *public* data, but some of it is *open*, meaning that it is accessible and available to *all* users; while some TCGA data is *controlled* and restricted to authorized users.
* **Public Data** Sometimes the word "public" is misinterpreted as meaning "open". All of the TCGA data is *public* data, and much of it is *open*, meaning that it is accessible and available to *all* users; while some low-level TCGA data is *controlled* and restricted to authorized users.
* **Open-Access Data** Depending on how you categorize the data, *most* of the TCGA data is open-access data. This includes all de-identified clinical and biospecimen data, as well as all Level-3 molecular data including gene expression data, DNA methylation data, DNA copy-number data, protein expression data, somatic mutation calls, etc.
* **Controlled-Access Data** All low-level sequence data (both DNA-seq and RNA-seq), the raw SNP array data (CEL files), germline mutation calls, and a small amount of other data are treated as *controlled* data and require that a user be properly authenticated and have dbGaP-authorization prior to access these data.

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