Update README.md

README.md

@@ -118,10 +118,9 @@ To view the summary information for a particular cluster or sample, enter "info
 
 *	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 
@@ -133,32 +132,32 @@ 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:  
-  *	**<cluster or sample ID>_Dendrogram.txt**
+  *	**\<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
+   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
+   2.	**\<cluster or sample ID>\_Group1_Interactions.txt:** network interaction matrix
 
-   3.	**<cluster or sample ID>_Group1.png:** image of the network
+   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)
-
-*	Output files can be opened from the GUI: select File > Open to open a file explorer window.
+ * *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.
 
 
 ## 4.	Change the Parameter Configuration and Re-run Proteinarium: