From 948f30141804fcf1e0445e60bc709f48c3080b54 Mon Sep 17 00:00:00 2001
From: aakan96 <aakan96@mi.fu-berlin.de>
Date: Fri, 21 Jul 2023 12:31:47 +0000
Subject: [PATCH] Update file mRNA_limma_dataset_svm_final.ipynb

---
 .../mRNA_limma_dataset_svm_final.ipynb        | 416 +-----------------
 1 file changed, 22 insertions(+), 394 deletions(-)

diff --git a/03_Machine_Learning/mRNA_limma_dataset_svm_final.ipynb b/03_Machine_Learning/mRNA_limma_dataset_svm_final.ipynb
index 950334d..46d1177 100644
--- a/03_Machine_Learning/mRNA_limma_dataset_svm_final.ipynb
+++ b/03_Machine_Learning/mRNA_limma_dataset_svm_final.ipynb
@@ -388,379 +388,7 @@
   },
   {
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@@ -821,7 +449,7 @@
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@@ -980,7 +608,7 @@
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@@ -991,7 +619,7 @@
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@@ -1016,7 +644,7 @@
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@@ -1026,7 +654,7 @@
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@@ -1064,7 +692,7 @@
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@@ -1104,7 +732,7 @@
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@@ -1132,7 +760,7 @@
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@@ -1159,7 +787,7 @@
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@@ -1188,7 +816,7 @@
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@@ -1202,7 +830,7 @@
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@@ -1212,7 +840,7 @@
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@@ -1222,7 +850,7 @@
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@@ -1250,7 +878,7 @@
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-- 
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