Submodule

paga-paul15.ipynb

@@ -7,6 +7,23 @@
     "# Trajectory inference for hematopoiesis in mouse"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    ":::{seealso}\n",
+    "More examples for trajectory inference on complex datasets can be found in the\n",
+    "[PAGA](https://github.com/theislab/paga) repository {cite-hack}`Wolf19`, for instance, multi-resolution analyses of whole\n",
+    "animals, such as for [planaria](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/planaria/planaria.ipynb) for data of {cite-hack}`Plass18`.\n",
+    "\n",
+    "\n",
+    "```{image} /_static/img/tutorials/paga_planaria.png\n",
+    ":width: 350px\n",
+    ":align: center\n",
+    "```\n",
+    ":::"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

pbmc3k.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Preprocessing and clustering 3k PBMCs"
+    "# Preprocessing and clustering 3k PBMCs (legacy workflow)"
    ]
   },
   {

spatial/basic-analysis.ipynb

@@ -28,7 +28,7 @@
    "metadata": {},
    "source": [
     "* This tutorial demonstrates how to work with spatial transcriptomics data within Scanpy.\n",
-    "* We focus on 10x Genomics [Visium](https://www.10xgenomics.com/spatial-transcriptomics/) data, and provide an example for [MERFISH](#merfish-example)."
+    "* We focus on 10x Genomics [Visium](https://www.10xgenomics.com/spatial-transcriptomics/) data, and provide an example for MERFISH."
    ]
   },
   {

spatial/integration-scanorama.ipynb

@@ -18,9 +18,10 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    ".. note::\n",
+    ":::{note}\n",
     "\n",
-    "   For up-to-date analysis tutorials, kindly check out [SquidPy tutorials](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/index.html)."
+    "   For up-to-date analysis tutorials, kindly check out [SquidPy tutorials](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/index.html).\n",
+    ":::"
    ]
   },
   {