From 73bbb3d7b99e9a5027f738f4cbe974646cd3ce73 Mon Sep 17 00:00:00 2001
From: MarcElosua <elosua.marc@gmail.com>
Date: Sun, 15 Jun 2025 18:55:52 -0400
Subject: [PATCH] notebook 8 edits

---
 Day2/08.motif_enrichment_analysis.ipynb | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/Day2/08.motif_enrichment_analysis.ipynb b/Day2/08.motif_enrichment_analysis.ipynb
index b63f75d..f8f3598 100644
--- a/Day2/08.motif_enrichment_analysis.ipynb
+++ b/Day2/08.motif_enrichment_analysis.ipynb
@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "39f086cc",
    "metadata": {
     "vscode": {
@@ -47,6 +47,18 @@
    },
    "outputs": [],
    "source": [
+    "if (!requireNamespace(\"JASPAR2020\", quietly = TRUE)) {\n",
+    "    BiocManager::install(\"JASPAR2020\")\n",
+    "}\n",
+    "\n",
+    "if (!requireNamespace(\"TFBSTools\", quietly = TRUE)) {\n",
+    "    BiocManager::install(\"TFBSTools\")\n",
+    "}\n",
+    "\n",
+    "if (!requireNamespace(\"ggseqlogo\", quietly = TRUE)) {\n",
+    "    BiocManager::install(\"ggseqlogo\")\n",
+    "}\n",
+    "\n",
     "library(Signac)\n",
     "library(Seurat)\n",
     "library(JASPAR2020)\n",
@@ -104,7 +116,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "5c2ed6ba-0038-4d00-8a29-efd61bedf0ff",
    "metadata": {
     "vscode": {
@@ -122,7 +134,7 @@
    ],
    "source": [
     "start_time <- Sys.time()\n",
-    "file <- \"PBMC_motif.rds\"\n",
+    "file <- \"data/day2/PBMC_motif.rds\"\n",
     "PBMC_obj <- readRDS(file)\n",
     "end_time <- Sys.time()\n",
     "cat(\"Loading time:\", end_time - start_time, \"seconds\\n\")\n"