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Revert "update tutorial with new download instructions"
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This reverts commit 70aa20c.
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@katosh
katosh committed Aug 21, 2024
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250 changes: 21 additions & 229 deletions notebooks/basic_tutorial.ipynb
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"source": [
"## Step 1: Reading and Displaying the Dataset\n",
"\n",
"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:"
"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."
]
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" obsp: 'DM_Kernel', 'DM_Similarity', 'connectivities', 'distances', 'knn'"
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"ad = sc.read(\"data/preprocessed_t-cell-depleted-bm-rna.h5ad\")\n",
"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"
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