♻️ Clean up and re-run

laminlabs · Jan 30, 2025 · d7ee08c · d7ee08c
1 parent 84357d9
commit d7ee08c
Showing 1 changed file with 1 addition and 30 deletions.
diff --git a/docs/cellxgene-curate.ipynb b/docs/cellxgene-curate.ipynb
@@ -414,36 +414,6 @@
     "artifact.describe()"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "3cf67f90",
-   "metadata": {},
-   "source": [
-    "The below is optional -- it mimics the way cellxgene creates collections of `AnnData` objects to link them to studies."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8940e83c",
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "# register a new collection\n",
-    "title = \"Cross-tissue immune cell analysis reveals tissue-specific features in humans (for test demo only)\"\n",
-    "collection = ln.Collection(\n",
-    "    [artifact],  # registered artifact above, can also pass a list of artifacts\n",
-    "    name=title,  # title of the publication\n",
-    "    description=\"10.1126/science.abl5197\",  # DOI of the publication\n",
-    "    reference=\"E-MTAB-11536\",  # accession number (e.g. GSE#, E-MTAB#, etc.)\n",
-    "    reference_type=\"ArrayExpress\",  # source type (e.g. GEO, ArrayExpress, SRA, etc.)\n",
-    ").save()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "9eea92a2",
@@ -463,6 +433,7 @@
    },
    "outputs": [],
    "source": [
+    "title = \"Cross-tissue immune cell analysis reveals tissue-specific features in humans (for test demo only)\"\n",
     "adata_cxg = curator.to_cellxgene_anndata(is_primary_data=True, title=title)\n",
     "adata_cxg"
    ]