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HTAN Notebooks
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`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**

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   * - 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>`_
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   * - 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>`_
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   * - 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>`_
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**Molecular and Cellular Data in HTAN**     

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   * - A Guide to HTAN Data
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/A_Guide_to_HTAN_Data.ipynb>`_
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   * - Analyzing HTAN scRNASeq Data Using CellTypist
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Analyzing_HTAN_scRNASeq_Data_Using_CellTypist.ipynb>`_
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   * - Exploring HTAN scRNA-seq data
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Investigating_Single_Cell_HTAN_Data.ipynb>`_
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   * - 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>`_
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   * - Exploring HTAN MIBI Imaging data
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Analyzing_HTAN_MIBI_Imaging_Data.ipynb>`_
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   * - Exploring Spatial Cellular and Molecular Relationships
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     - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/R%20Notebooks/Explore_HTAN_Spatial_Cellular_Relationships.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>`_
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**HTAN Processing and Workflows**

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   * - 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>`_
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   * - Creating CDS Data Import Manifests Using BQ
     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb>`_
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