box for deconvolution

theislab · Feb 19, 2025 · 9e9ebe3 · 9e9ebe3
1 parent 78722fe
commit 9e9ebe3
Showing 1 changed file with 54 additions and 20 deletions.
diff --git a/jupyter-book/deconvolution/bulk_deconvolution.ipynb b/jupyter-book/deconvolution/bulk_deconvolution.ipynb
@@ -7,6 +7,56 @@
     "# Bulk deconvolution"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "```{dropdown} <i class=\"fas fa-brain\"></i>&nbsp;&nbsp;&nbsp;Key takeaways\n",
+    "\n",
+    ":::{card}\n",
+    ":link: deconvolution-bulk-deconvolution-key-takeaway-1\n",
+    ":link-type: ref\n",
+    "Use unbiased reference data with no missing cell type.\n",
+    ":::\n",
+    "\n",
+    ":::{card}\n",
+    ":link: deconvolution-bulk-deconvolution-key-takeaway-2\n",
+    ":link-type: ref\n",
+    "Normalize the reference data using library size normalization.\n",
+    ":::\n",
+    "\n",
+    ":::{card}\n",
+    ":link: deconvolution-bulk-deconvolution-key-takeaway-3\n",
+    ":link-type: ref\n",
+    "Feature selection prior deconvolution improves the accuracy of the results particularly for linear deconvolution methods. \n",
+    ":::\n",
+    "\n",
+    ":::{card}\n",
+    ":link: deconvolution-bulk-deconvolution-key-takeaway-4\n",
+    ":link-type: ref\n",
+    "Deconvolution is a challenging task (see limitations and traps). Therefore, we recommend the users to try more than one deconvolution method and select one after assessing the results biologically.\n",
+    ":::\n",
+    "\n",
+    "```\n",
+    "\n",
+    "``````{dropdown} <i class=\"fa-solid fa-gear\"></i>&nbsp;&nbsp;&nbsp;Environment setup\n",
+    "`````{tab-set}\n",
+    "   \n",
+    "````{tab-item} Steps\n",
+    "```{include} ../_static/default_text_env_setup.md\n",
+    "```\n",
+    "````\n",
+    "\n",
+    "````{tab-item} yml\n",
+    "```{literalinclude} differential_gene_expression.yml\n",
+    ":language: yaml\n",
+    "```\n",
+    "````\n",
+    "\n",
+    "`````\n",
+    "``````"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -18,6 +68,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "(deconvolution-bulk-deconvolution-key-takeaway-1)=\n",
     "## Background"
    ]
   },
@@ -350,6 +401,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "(deconvolution-bulk-deconvolution-key-takeaway-2)=\n",
     "### Visualization of single-cell data"
    ]
   },
@@ -2410,6 +2462,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "(deconvolution-bulk-deconvolution-key-takeaway-3)=\n",
+    "(deconvolution-bulk-deconvolution-key-takeaway-4)=\n",
     "## Limitations and traps"
    ]
   },
@@ -2443,26 +2497,6 @@
     "By focusing on the variation within cell types, and less between cell types (as most deconvolution methods), CPM can discover changes in compositions of distinct subgroups of cells or continuous changes across specific cellular trajectories. "
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Key takeaways"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "1. Use unbiased reference data with no missing cell type.\n",
-    "\n",
-    "2. Normalize the reference data using library size normalization.\n",
-    "\n",
-    "3. Feature selection prior deconvolution improves the accuracy of the results particularly for linear deconvolution methods. \n",
-    "\n",
-    "Deconvolution is a challenging task (see limitations and traps). Therefore, we recommend the users to try more than one deconvolution method and select one after assessing the results biologically.\n"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},