Merge pull request #687 from isb-cgc/staging

Staging

docs/source/index.rst

@@ -59,6 +59,7 @@ The `ISB-CGC <https://isb-cgc.org>`_ aims to serve the needs of a broad range of
    sections/HowTos
    sections/RegulomeExplorerNotebooks
    sections/MachineLearningNotebooks
+   sections/HTANNotebooks
    sections/TutorialsAndHow-ToGuides
    sections/Releases
    sections/Quick-links-updated

docs/source/sections/HTANNotebooks.rst

@@ -0,0 +1,21 @@
+**************************
+HTAN Notebooks
+**************************
+
+`HTAN <https://humantumoratlas.org/>`_ is a National Cancer Institute (NCI)-funded Cancer Moonshot initiative to construct 3-dimensional atlases of the dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease (`Cell April 2020 <https://www.sciencedirect.com/science/article/pii/S0092867420303469>`_).
+
+.. list-table:: 
+   :widths: 100 10 10
+   :align: center
+   :header-rows: 0
+
+   * - Investigating HTAN scRNA-seq with BigQuery
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Building_AnnData_with_Subset_of_Cells_from_BQ.ipynb>`_
+     -  
+   * - Explore HTAN single cell RNA seq data
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Investigating_Single_Cell_HTAN_Data.ipynb>`_
+     - 
+   * - Explore HTAN Clinicial, Biospecimen, and Assay Metadata
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Explore_HTAN_Clinical_Biospecimen_Assay_Metadata.ipynb>`_
+     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/R%20Notebooks/Explore_HTAN_Clinical_Biospecimen_Assay_Metadata.md>`_
+

docs/source/sections/Hosted-Data.rst

@@ -222,13 +222,18 @@ From Other Sources
      - 
      - |checkmark|
      - 
+   * - `HTAN <data/HTAN_about.html>`_
+     - 
+     - |checkmark|
+     - 
 
 .. toctree::
    :maxdepth: 1
    :hidden:
 
    data/COSMIC_about
    PanCancer-Atlas-Mirror
+   data/HTAN_about
 
 Reference Data Sets
 -------------------

docs/source/sections/data/HTAN_about.rst

@@ -0,0 +1,28 @@
+*****************
+HTAN Data Set
+*****************
+
+About HTAN
+------------------------------------------------------------------------
+
+The Human Tumor Atlas Network (`HTAN <https://humantumoratlas.org/>`_) is focused on transitions in cancer. Funded by the National Cancer Institute (NCI) Cancer Moonshot initiative, its mission is to construct three-dimensional atlases of the dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease (`Cell April 2020 <https://www.sciencedirect.com/science/article/pii/S0092867420303469>`_). Many HTAN studies focus on single cell and multiplex imaging modalities.
+
+
+About the HTAN Data
+---------------------------------------------------------------------------------
+
+HTAN data encompasses at least 11 atlases and 17 primary tumor sites.
+Data (Release 2) was extracted from the HTAN Data Portal via Synapse (https://humantumoratlas.org/data-download).
+
+To explore HTAN data, please see the `HTAN Data Portal <https://humantumoratlas.org/explore/>`_.
+
+
+Accessing the HTAN Data in Google BigQuery
+------------------------------------------------
+
+ISB-CGC has HTAN data, such as single cell RNA-Seq, clinical, biospecimen, and metadata, stored in Google BigQuery tables. Information about these tables can be found using the `ISB-CGC BigQuery Table Search <https://isb-cgc.appspot.com/bq_meta_search/>`_ with HTAN selected for filter PROGRAM. To learn more about this tool, see the `ISB-CGC BigQuery Table Search documentation <../BigQueryTableSearchUI.html>`_.
+
+The HTAN tables are in project isb-cgc-bq. To learn more about how to view and query tables in the Google BigQuery console, see the `ISB-CGC BigQuery Tables documentation <../BigQuery.html>`_.
+
+- Data set ``isb-cgc-bq.HTAN`` contains the latest tables for each data type.
+- Data set ``isb-cgc-bq.HTAN_versioned`` contains previously released tables, as well as the most current table.