added glmPCA notebooks

bhardwaj-lab · Nov 5, 2023 · 3250490 · 3250490
1 parent 7130fad
commit 3250490
Show file tree

Hide file tree

Showing 5 changed files with 18 additions and 1 deletion.
diff --git a/docs/conf.py b/docs/conf.py
@@ -55,9 +55,13 @@ def get_version(path=VPATH):
     "sphinx.ext.autosummary",
     "sphinxarg.ext",
     "sphinx_toolbox.collapse",
+    'nbsphinx',
 ]
 #    'numpydoc'
 
+# Do not execute tutorial notebooks
+nbsphinx_execute = 'never'
+
 # This is needed to suppress autosummary reordering
 numpydoc_show_class_members = False
 

diff --git a/docs/content/tutorials.rst b/docs/content/tutorials.rst
@@ -1,9 +1,21 @@
 Tutorials
 ===========
 
+Tutorials for using sincei on the command line
+-----------------------------------------------
+
 .. toctree::
     :maxdepth: 1
 
     tutorials/sincei_tutorial_sortChIC.rst
     tutorials/sincei_tutorial_10x.rst
     tutorials/sincei_tutorial_10xATAC.rst
+
+Tutorials for using sincei inside python
+-----------------------------------------
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/snmC2Tseq_preprocessing
+    tutorials/GLM_PCA_analysis
diff --git a/tutorial/GLM_PCA_analysis.ipynb → .../content/tutorials/GLM_PCA_analysis.ipynb b/tutorial/GLM_PCA_analysis.ipynb → .../content/tutorials/GLM_PCA_analysis.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "source": [
     "# Tutorial for snmC2Tseq\n",
-    "Using the single-cell methylation data from snmC2Tseq [1], we re-procwessed the dataset to extract smaller bins (10kb), yielding non-Gaussian data. The data is losely following a Beta distribution, and we thus employ GLM-PCA with Beta distribution to find a lower-dimension representation.\n",
+    "Using the single-cell methylation data from snmC2Tseq [1], we re-processed the dataset to extract smaller bins (10kb), yielding non-Gaussian data. The data is losely following a Beta distribution, and we thus employ GLM-PCA with Beta distribution to find a lower-dimension representation.\n",
     "<br/>\n",
     "[1]: https://www.sciencedirect.com/science/article/pii/S2666979X22000271?via%3Dihub"
    ]

diff --git a/tutorial/snmC2Tseq_preprocessing.ipynb → ...t/tutorials/snmC2Tseq_preprocessing.ipynb b/tutorial/snmC2Tseq_preprocessing.ipynb → ...t/tutorials/snmC2Tseq_preprocessing.ipynb
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,4 +2,5 @@ sphinx >=5.0
 sphinx-argparse >=0.2.5
 sphinx-toolbox
 sphinx_rtd_theme
+nbsphinx
 numpydoc