Update README.md

README.md

@@ -98,31 +98,31 @@ To view the summary information for a particular cluster or sample, enter "info
 
 ## 2.	Running Proteinarium 
 
-*Selecting Files*
+###*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*
-*	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.  
+###*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. 
+*	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. 
 
- o	**<projectName>_ClusterAnalyses.csv:** cluster analysis files
+ **	**<projectName>_ClusterAnalyses.csv:** cluster analysis files
 
- o	**<projectName>_Dendrogram.png:** dendrogram image
+ **	**<projectName>_Dendrogram.png:** dendrogram image
 
- o	**<projectName>_Dendrogram.txt:** representation of the dendrogram in Newick tree format 
+ **	**<projectName>_Dendrogram.txt:** representation of the dendrogram in Newick tree format 
 
 
 ## 3.	Viewing Clusters 
@@ -134,9 +134,9 @@ To view the summary information for a particular cluster or sample, enter "info
 *	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:  
- o	**<cluster or sample ID>_Dendrogram.txt**
+ **	**<cluster or sample ID>_Dendrogram.txt**
 
- o	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:
+ **	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