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genepattern · Mar 21, 2018 · 3a58eb3 · 3a58eb3
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diff --git a/Single-Cell RNA-seq Clustering Analysis Notebook.ipynb b/Single-Cell RNA-seq Clustering Analysis Notebook.ipynb
@@ -20,19 +20,19 @@
     "\n",
     "### Analysis Overview\n",
     "\n",
-    "1. <a href=\"#Step-1:-Setup-Analysis\">**Setup Analysis**</a>\n",
+    "1. [**Setup Analysis**](#Step-1:-Setup-Analysis)\n",
     "    1. Load raw count matrix.\n",
-    "2. <a href=\"#Step-2:-Preprocess-Counts\">**Preprocess Counts**</a>\n",
+    "2. [**Preprocess Counts**](#Step-2:-Preprocess-Counts)\n",
     "    1. Filter cells based on QC metrics.\n",
     "    2. Perform data normalization and scaling.\n",
     "    3. Remove unwanted sources of variation (number of detected molecules per cell as well as the percentage mitochondrial gene content).\n",
     "    4. Detect highly variable genes.\n",
     "    5. Perform linear dimensional reduction (PCA).\n",
-    "3. <a href=\"#Step-3:-Cluster-Cells\">**Cluster Cells**</a>\n",
+    "3. [**Cluster Cells**](#Step-3:-Cluster-Cells)\n",
     "    1. Cluster cells (graph-based clustering) in PCA space and visualize using t-SNE.\n",
-    "4. <a href=\"#Step-4:-Visualize-Cluster-Markers\">**Visualize Cluster Markers**</a>\n",
+    "4. [**Visualize Cluster Markers**](#Step-4:-Visualize-Cluster-Markers)\n",
     "    1. Explore and visualize cluster markers interactively.\n",
-    "5. <a href=\"#Step-5:-Export-Analysis-Data\">**Export Analysis Data**</a>\n",
+    "5. [**Export Analysis Data**](#Step-5:-Export-Analysis-Data)\n",
     "    1. Export data to `.csv` files or a compressed `.h5ad` format."
    ]
   },

diff --git a/__init__.py b/__init__.py