add file to aws

Author: marouenbg

netbooks/netZooR/sex_differences_LUAD.ipynb

@@ -26,6 +26,22 @@
     "\n",
     "The LUAD data used is provided from TCGA<sup>3</sup>, a NIH project that has gathered gene expression data from various cancer types. The normal lung data is from GTEx<sup>4</sup>. \n",
     "\n",
+    "This analysis can be ran on the server or locally by setting the following parameter."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "runserver=1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "### Loading libraries "
    ]
   },
@@ -68,7 +84,18 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Here we will load a table with gene Ensembl ID and HGNC from GENCODE V22. We will use this to convert Ensembl IDs to HGNC, required for gene set enrichment analysis."
+    "Here we will load a table with gene Ensembl ID and HGNC from GENCODE V22. We will use this to convert Ensembl IDs to HGNC, required for gene set enrichment analysis. Let's first download the annotation file."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if(runserver==0){\n",
+    "    system(\"curl -O https://netzoo.s3.us-east-2.amazonaws.com/netbooks/lungcancer/gencode_annotation_v22_complete.txt\")\n",
+    "}"
    ]
   },
   {
@@ -1138,7 +1165,7 @@
    "mimetype": "text/x-r-source",
    "name": "R",
    "pygments_lexer": "r",
-   "version": "4.1.1"
+   "version": "4.2.2"
   }
  },
  "nbformat": 4,