Merge pull request #762 from isb-cgc/master

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isb-cgc · Mar 12, 2024 · 9d67ee1 · 9d67ee1
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diff --git a/docs/source/sections/HTANNotebooks.rst b/docs/source/sections/HTANNotebooks.rst
@@ -4,33 +4,57 @@ 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>`_).
 
+
+**HTAN Clinical, Biospecimen, and Assay File Annotation Data**
+
 .. list-table:: 
    :widths: 95 15 10
    :align: center
    :header-rows: 0
-   
-   * - Integrating Controlled and Open Access 10X Visium Data in SB-CGC Data Studio
-     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Analyzing_HTAN_Data_in_SB_Data_Studio.ipynb>`_
-     - 
+
+   * - Exploring HTAN Clinical, 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>`_
    * - Utilizing the HTAN ID Provenance Google BigQuery Table
      - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/HTAN_ID_Provenance_In_BQ.ipynb>`_
      - 
-   * - Constructing AnnData Objects with scRNA-seq Data from BigQuery
-     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Building_AnnData_with_Subset_of_Cells_from_BQ.ipynb>`_
-     -  
-   * - Exploring HTAN scRNA-seq data
-     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Investigating_Single_Cell_HTAN_Data.ipynb>`_
-     - 
    * - Identifying Assay Data by Primary Organ Type in ISB-CGC
      - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Identifying_HTAN_Data_Files_by_Organ_in_ISB_CGC.ipynb>`_
      - 
+   * - Identifying and Compiling Precancer Cases and Samples in HTAN
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Identifying_and_Compiling_Precancer_Cases_and_Samples_in_HTAN.ipynb>`_
+     - 
+
+**Molecular and Cellular Data in HTAN**     
+
+.. list-table:: 
+   :widths: 95 15 10
+   :align: center
+   :header-rows: 0
+
+   * - Exploring HTAN scRNA-seq data
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Investigating_Single_Cell_HTAN_Data.ipynb>`_
+     - 
+   * - Constructing AnnData Objects with scRNA-seq Data from BigQuery
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Building_AnnData_with_Subset_of_Cells_from_BQ.ipynb>`_
+     -  
    * - Exploring HTAN MIBI Imaging data
      - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Analyzing_HTAN_MIBI_Imaging_Data.ipynb>`_
      - 
    * - Exploring Spatial Cellular and Molecular Relationships
      - 
      - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/R%20Notebooks/Explore_HTAN_Spatial_Cellular_Relationships.md>`_
-   * - Exploring HTAN Clinical, 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>`_
+   * - Analyzing HTAN Spatial data with BigQuery Geospatial Analytics
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Analyzing_HTAN_spatial_data_with_BigQuery_geospatial_analytics.ipynb>`_
+     -        
+
+**HTAN Processing and Workflows**
 
+.. list-table:: 
+   :widths: 95 15 10
+   :align: center
+   :header-rows: 0
+
+   * - Integrating Controlled and Open Access 10X Visium Data in SB-CGC Data Studio
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Analyzing_HTAN_Data_in_SB_Data_Studio.ipynb>`_
+     -