Update GO_Enrichment_Analysis.ipynb

welch-lab · Feb 26, 2022 · e7360cb · e7360cb
1 parent 1f41fe4
commit e7360cb
Showing 1 changed file with 33 additions and 6 deletions.
diff --git a/GO_Enrichment_Analysis.ipynb b/GO_Enrichment_Analysis.ipynb
@@ -1,5 +1,34 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "95aa70a3",
+   "metadata": {},
+   "source": [
+    "This notebook demonstrates the usage of the pyliger functions of running GO enrichment analysis."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "d88b7404",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Please load following modules\n",
+    "import os\n",
+    "import pyliger"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d9bf3c64",
+   "metadata": {},
+   "source": [
+    "1. We use the same data as used in [GOATOOLS tutorial](https://github.com/tanghaibao/goatools/blob/main/notebooks/goea_nbt3102.ipynb). It is from a 2014 Nature paper:\n",
+    "[Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells](https://www.nature.com/articles/nbt.3102#methods)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -17,7 +46,7 @@
    "source": [
     "from genes_ncbi_10090_proteincoding import GENEID2NT as GeneID2nt_mus\n",
     "# Data will be stored in this variable\n",
-    "import os\n",
+    "\n",
     "geneid2symbol = {}\n",
     "# Get xlsx filename where data is stored\n",
     "ROOT = os.path.dirname(os.getcwd()) # go up 1 level from current working directory\n",
@@ -39,13 +68,11 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "d88b7404",
+   "cell_type": "markdown",
+   "id": "ebf90fb4",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "import pyliger"
+    "`run_GO_analysis` requires three inputs: 1. a list of study genes; 2. a list of background genes; 3. data source (currently, PyLiger supports two data sources - human or mouse)."
    ]
   },
   {