From 4211de33601de6c40bee06cc8c75b9058d5373d4 Mon Sep 17 00:00:00 2001
From: gwaygenomics <gregory.way@gmail.com>
Date: Sat, 26 Jan 2019 11:06:11 -0500
Subject: [PATCH] add gtex and tcga to analysis pipelin

---
 analysis-pipeline.sh | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/analysis-pipeline.sh b/analysis-pipeline.sh
index 7aa615eb8..48c9c9f1a 100644
--- a/analysis-pipeline.sh
+++ b/analysis-pipeline.sh
@@ -41,7 +41,7 @@ bash stability_analysis.sh
 ##############################
 # Step 4: Analyze Weights (Module 6)
 ##############################
-cd ../6.analyze-weights
+cd ../6.biobombe-projection
 
 # Project the networks onto the compressed weight matrices to derive biological insight
 python interpret-compression.py
@@ -52,4 +52,21 @@ python interpret-compression.py
 cd ../7.analyze-coverage
 
 # Project the networks onto the compressed weight matrices to derive biological insight
-python coverage-analysis.py
+bash run_coverage_analysis.sh
+
+##############################
+# Step 6: Perform GTEx module interpretation of increased blood correlation
+##############################
+cd ../8.gtex-interpret
+
+# Determine the difference between VAE models k = 2 and k = 3 and apply features to
+# external datasets
+bash gtex_analysis.sh
+
+##############################
+# Step 7: Perform the TCGA classification analysis predicting cancer type and mutations
+##############################
+cd ../9.tcga-classify
+
+# Train several models and visualize results
+bash classify_analysis.sh