From bccc9cac80426b39e523c6682731fbb1adf9aafa Mon Sep 17 00:00:00 2001
From: jschust <53572903+jschust@users.noreply.github.com>
Date: Wed, 1 Jul 2020 11:08:40 -0400
Subject: [PATCH] Update README.md

---
 README.md | 39 ++++++++++++++++++++-------------------
 1 file changed, 20 insertions(+), 19 deletions(-)

diff --git a/README.md b/README.md
index 4203e08..1285bb7 100644
--- a/README.md
+++ b/README.md
@@ -56,7 +56,7 @@ This option is provided primarily for scripting purposes; it is instead recommen
 
 For a complete list of configuration options and explanations of how they affect Proteinarium, refer to [Configuration](Configuration.pdf).
 
-## Output
+### Output
 All output files go to the folder specified by the `outputDirectory` configuration option. By default, this goes to a folder called `output` in the same directory that you run Proteinarium from.
 * **\<projectName\>_ClusterAnalyses.csv**: cluster analysis files
 * **\<projectName\>_Dendrogram.png**: dendrogram image
@@ -87,7 +87,7 @@ To view the summary information for a particular cluster or sample, enter "info
 * *Group 2 Patients* (Sample IDs of the individuals)
 **Note**: the above information is available for all patients at any time in the **\<projectName\>_ClusterAnalyses.csv** output file.
 
-
+----------------------------------------------
 ## Running Proteinarium with Graphical User Interface (GUI)
 
 ## 1.	Getting Started
@@ -98,21 +98,22 @@ To view the summary information for a particular cluster or sample, enter "info
 
 ## 2.	Running Proteinarium 
 
-Selecting Files
-•	In the GUI, select File > New analysis 
+* *Selecting Files*
+
+•	In the GUI, select **File > New analysis** 
 
 •	Choose the data files for upload.  If you are only analyzing one group or a single sample, leave the Geneset File 2 file field empty. NOTE: If you would like to select new Gene Set Files, click on the “Clear Gene Files” button before selecting new Gene Set Files. 
 
 •	Enter a Project Name into the field “Project Name”.  If left blank, the program default to the project name “SIM” 
 
-Setting Parameters – Configuration File
+* *Setting Parameters – Configuration File*
 •	Before running Proteinarium, confirm or make changes to the program’s configurable parameters.  A table with all possible parameters, their definitions and their default settings are provided by selecting Help > Available Configurations.  
 
 •	Select File > Settings or “Settings” button to view and change parameters.  If any changes are made click “Apply Changes” before exiting. NOTE: The values of the parameters for a New Analysis are not all set to the Default values. These are the values used in our testing and validation with bootstrapping turned off (ie 0 iterations). 
 
 •	For Advance Settings Select File > Settings and click on the “Advance Settings” button. Once changed click on “Set Settings” and the “Apply Changes” buttons. 
 
-Running Proteinarium
+* *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. 
@@ -144,19 +145,19 @@ Running Proteinarium
    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. 
-o	Average Distance (Height)
-o	Bootstrapping Confidence
-o	Total Number of Samples
-o	Number in Group 1 (number of samples)
-o	Number in Group 2 (number of samples)
-o	p-value (Fisher Exact test for Group 1 and Group 2)
-o	Group 1 and Group 2 Clustering Coefficient
-o	Group 1 Clustering Coefficient
-o	Group 2 Clustering Coefficient
-o	Group 1 minus Group 2 Clustering Coefficient
-o	Group 2 minus Group 1 Clustering Coefficient
-o	Group 1 Patients (Sample IDs of the individuals)
-o	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.