From bc1ed29d902c28c731511c5ebf1141e8d4333459 Mon Sep 17 00:00:00 2001
From: jschust <53572903+jschust@users.noreply.github.com>
Date: Wed, 1 Jul 2020 11:55:47 -0400
Subject: [PATCH] Update README.md

---
 README.md | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/README.md b/README.md
index d9c3a5e..8ab5bee 100644
--- a/README.md
+++ b/README.md
@@ -116,9 +116,9 @@ To view the summary information for a particular cluster or sample, enter "info
 ### Running Proteinarium
 *	Once files are uploaded and parameters are set, click “Run Proteinarium”
 *	If more than one sample is contained within the input file (s), the dendrogam will be displayed.  All output files generated by Proteinarium will be saved to the folder specified by the outputDirectory configuration option. By default, this goes to a folder called “Output” in the same directory as the Proteinarium.jar file. 
-  * **\<projectName>\_ClusterAnalyses.csv:** cluster analysis files
-  * **\<projectName>\_Dendrogram.png:** dendrogram image
-  * **\<projectName>\_Dendrogram.txt:** representation of the dendrogram in Newick tree format 
+     * **\<projectName>\_ClusterAnalyses.csv:** cluster analysis files
+     * **\<projectName>\_Dendrogram.png:** dendrogram image
+     * **\<projectName>\_Dendrogram.txt:** representation of the dendrogram in Newick tree format 
     
     
 ## 3.	Viewing Clusters 
@@ -127,25 +127,25 @@ To view the summary information for a particular cluster or sample, enter "info
 *	Enter sample ID or branch number (ex: C12) in the space provided. 
 *	Select either “View Cluster” or “Get Cluster Information”.  
 *	If “View Cluster” is selected, the corresponding the output files will be available in the \<outputDirectory\>/<cluster or sample ID\> folder. And the following files are generated:  
- *	**\<cluster or sample ID>\_Dendrogram.txt**
- *	For each of the five possible output networks--Group 1, Group 2, [Group 1 + Group 2], [Group 1 - Group 2], [Group 2 - Group 1], three files are generated to summarize that network. For example:
-    1.	**\<cluster or sample ID>\_Group1_GeneSet.txt:** list of genes in the network and information about which input set they originated from (i.e. from Group 1, Group 2, or imputed from the interactome) and on how many samples the gene was found
-    2.	**\<cluster or sample ID>\_Group1_Interactions.txt:** network interaction matrix
-    3.	**\<cluster or sample ID>\_Group1.png:** image of the network
+    *	**\<cluster or sample ID>\_Dendrogram.txt**
+    *	For each of the five possible output networks--Group 1, Group 2, [Group 1 + Group 2], [Group 1 - Group 2], [Group 2 - Group 1], three files are generated to summarize that network. For example:
+        1.	**\<cluster or sample ID>\_Group1_GeneSet.txt:** list of genes in the network and information about which input set they originated from (i.e. from Group 1, Group 2, or imputed from the interactome) and on how many samples the gene was found
+        2.	**\<cluster or sample ID>\_Group1_Interactions.txt:** network interaction matrix
+        3.	**\<cluster or sample ID>\_Group1.png:** image of the network
 *	If “Get Cluster Information” is selected, the following information will be appended to the file “SystemsOutput.txt” as indicated by the text box of the GUI. 
- * *Average Distance (Height)*
- * *Bootstrapping Confidence*
- * *Total Number of Samples*
- * *Number in Group 1* (number of samples)
- * *Number in Group 2* (number of samples)
- * *p-value (Fisher Exact test for Group 1 and Group 2)*
- * *Group 1 and Group 2 Clustering Coefficient*
- * *Group 1 Clustering Coefficient*
- * *Group 2 Clustering Coefficient*
- * *Group 1 minus Group 2 Clustering Coefficient*
- * *Group 2 minus Group 1 Clustering Coefficient*
- * *Group 1 Patients* (Sample IDs of the individuals)
- * *Group 2 Patients* (Sample IDs of the individuals)
+    * *Average Distance (Height)*
+    * *Bootstrapping Confidence*
+    * *Total Number of Samples*
+    * *Number in Group 1* (number of samples)
+    * *Number in Group 2* (number of samples)
+    * *p-value (Fisher Exact test for Group 1 and Group 2)*
+    * *Group 1 and Group 2 Clustering Coefficient*
+    * *Group 1 Clustering Coefficient*
+    * *Group 2 Clustering Coefficient*
+    * *Group 1 minus Group 2 Clustering Coefficient*
+    * *Group 2 minus Group 1 Clustering Coefficient*
+    * *Group 1 Patients* (Sample IDs of the individuals)
+    * *Group 2 Patients* (Sample IDs of the individuals)
 *	Output files can be opened from the GUI: select **File > Open** to open a file explorer window.