update tutorial with new download instructions

settylab · Aug 12, 2024 · 70aa20c · 70aa20c
1 parent c654818
commit 70aa20c
Showing 1 changed file with 229 additions and 21 deletions.
diff --git a/notebooks/basic_tutorial.ipynb b/notebooks/basic_tutorial.ipynb
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@@ -108,20 +108,34 @@
    "source": [
     "## Step 1: Reading and Displaying the Dataset\n",
     "\n",
-    "We will start by loading the scRNA-seq dataset. For this demonstration, we will use the preprocessed T-cell depleted bone marrow data as described in the Mellon manuscript."
+    "We will start by loading the sc## Step 1: Reading and Displaying the Dataset\n",
+    "\n",
+    "We will start by loading the scRNA-seq dataset. For this demonstration, we will use the preprocessed T-cell depleted bone marrow data as described in the Mellon manuscript.\n",
+    "\n",
+    "### Download the Dataset\n",
+    "\n",
+    "First, download the dataset manually from the following Google Drive link:\n",
+    "\n",
+    "[Download preprocessed T-cell depleted bone marrow dataset](https://drive.google.com/uc?export=download&id=1eW79vxKafjNqOyRM6r0ocgnGwgN630CQ)\n",
+    "\n",
+    "After clicking the link, you may encounter a warning about the file size being too large for Google to scan for viruses. Click **Download anyway** to proceed with the download.\n",
+    "\n",
+    "### Load the Dataset\n",
+    "\n",
+    "Once downloaded, place the file in the `data/` directory of your project. Now, you can load the dataset using the following Python code:"
    ]
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@@ -139,14 +153,13 @@
        "    obsp: 'DM_Kernel', 'DM_Similarity', 'connectivities', 'distances', 'knn'"
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-    "ad_url = \"https://fh-pi-setty-m-eco-public.s3.amazonaws.com/mellon-tutorial/preprocessed_t-cell-depleted-bm-rna.h5ad\"\n",
-    "ad = sc.read(\"data/preprocessed_t-cell-depleted-bm-rna.h5ad\", backup_url=ad_url)\n",
+    "ad = sc.read(\"data/preprocessed_t-cell-depleted-bm-rna.h5ad\")\n",
     "ad"
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