Merge pull request #754 from isb-cgc/Deena-Staging-Theme

Deena staging theme
isb-cgc · Jan 17, 2024 · 7724aac · 7724aac
2 parents a0e8d12 + 49ce833
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diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1,3 @@
-sphinx==4.2.0
-docutils==0.16
+sphinx==6.2.1
+sphinx-rtd-theme==1.2.2
+docutils==0.18.1
diff --git a/docs/source/sections/HTANNotebooks.rst b/docs/source/sections/HTANNotebooks.rst
@@ -5,7 +5,7 @@ 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>`_).
 
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@@ -22,7 +22,7 @@ HTAN Notebooks
      - `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>`_
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Identifying_HTAN_Data_Files_by_Organ_in_ISB_CGC.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>`_

diff --git a/docs/source/sections/HowTos.rst b/docs/source/sections/HowTos.rst
@@ -12,7 +12,7 @@ I'm a novice, how do I...
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@@ -66,7 +66,7 @@ I'm an advanced user, how do I...
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diff --git a/docs/source/sections/MachineLearningNotebooks.rst b/docs/source/sections/MachineLearningNotebooks.rst
@@ -4,7 +4,7 @@ Machine Learning Notebooks
 Machine learning methods have enabled researchers to leverage and integrate the vast amounts of diverse cancer data to reveal new insights, develop better diagnostics, and improve therapy. ISB-CGC offers examples of how to use Google Cloud resources to train and use machine learning models for a variety of cancer applications and datasets.
 
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diff --git a/docs/source/sections/MitelmanDBNotebooks.rst b/docs/source/sections/MitelmanDBNotebooks.rst
@@ -5,7 +5,7 @@ MitelmanDB Notebooks
 The `Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer <https://mitelmandatabase.isb-cgc.org/>`_  is devoted to genes, chromosomes, and cancer. The Mitelman Database is supported by NCI (National Cancer Institute), the Swedish Cancer Society and the Swedish Childhood Cancer. `The Mitelman Database <https://mitelmandatabase.isb-cgc.org/>`_ is available from ISB-CGC to access and search the data.
 
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diff --git a/docs/source/sections/RegulomeExplorerNotebooks.rst b/docs/source/sections/RegulomeExplorerNotebooks.rst
@@ -6,7 +6,7 @@ Integrated statistical analysis and exploration of multiple genomic and clinical
 Bioinformatics notebooks
 =======================
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diff --git a/docs/source/sections/ReleaseNotes/ISB-CGCDataReleases.rst b/docs/source/sections/ReleaseNotes/ISB-CGCDataReleases.rst
@@ -4,7 +4,7 @@ ISB-CGC Data Release Notes
 
 *September 16, 2023*
 
-New masked somatic mutation data added to isb-cgc-bq for GDC release 37
+New masked somatic mutation data added to isb-cgc-bq for GDC release 37.
 
 **BigQuery tables created**
 

diff --git a/docs/source/sections/ReleaseNotes/MitelmanReleaseNotes.rst b/docs/source/sections/ReleaseNotes/MitelmanReleaseNotes.rst
@@ -6,6 +6,16 @@ To search this database hosted by the ISB-CGC, please visit `Mitelman Database o
 
 For more detailed information about the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer, see `Mitelman Database <https://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/data/Mitelman_about.html>`_.
 
+*January 16, 2024*
+
+Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer quarterly update.
+
+**Updated totals**
+
+- Total number of cases 77,532
+- Total number of unique gene fusions 33,802
+- Total number of genes involved 14,051
+
 *October 16, 2023*
 
 Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer quarterly update.

diff --git a/docs/source/sections/ReleaseNotes/WebAppReleaseNotes.rst b/docs/source/sections/ReleaseNotes/WebAppReleaseNotes.rst
@@ -2,6 +2,9 @@
 ISB-CGC Web App Release Notes
 #############################
 
+*November 27, 2023* 
+
+- On the ISB-CGC Help-->Video Tutorials page, the Introduction video has been replaced with a new version. Two obsolete videos "Image Viewers" and "Exporting Cohort" were removed.
 
 *May 3, 2023*