README corrections.

README.md

@@ -1,38 +1,38 @@
 # TriPOINT
 A pathway analysis tool that integrates non-coding regulators for further gene prioritization.
 
-Binary file: tripoint.jar
+**Binary** file: tripoint.jar
 
 Available datasets are in the data directory.
 
-Usage: java -jar tripoint.jar <expression file> -db <pathway database> -o <output directory>
+**Usage:** java -jar tripoint.jar <expression file> -db <pathway database> -o <output directory>
 
 #Parameters
 
--db	Sets pathway database to import pathways from GRAPHITE.  Values available: "kegg", "reactome", "biocarta", "humancyc", "nci", "panther"
+**-db**	Sets pathway database to import pathways from GRAPHITE.  Values available: "kegg", "reactome", "biocarta", "humancyc", "nci", "panther"
 
--o	Sets output directory for saving result files.  REQUIRED
+**-o**	Sets output directory for saving result files.  REQUIRED
 
--gid	Sets the conversion method for gene identifiers.  Refer to 'convertIdentifiers' in GRAPHITE. Default: "SYMBOL" (Currently other identifiers are not recommended)
+**-gid**	Sets the conversion method for gene identifiers.  Refer to 'convertIdentifiers' in GRAPHITE. Default: "SYMBOL" (Currently other identifiers are not recommended)
 
--up	Sets the up-regulated gene threshold.  Default: 0.05
+**-up**	Sets the up-regulated gene threshold.  Default: 0.05
 
--down	Sets the down-regulated gene threshold.  Default: -0.05
+**-down**	Sets the down-regulated gene threshold.  Default: -0.05
 
--w	Sets the weak activation/inhibition factor.  Default: 0.5
+**-w**	Sets the weak activation/inhibition factor.  Default: 0.5
 
--p	Controls the impact of gene expression when calculating measures.  Default: 0.25
+**-p**	Controls the impact of gene expression when calculating measures.  Default: 0.25
 
--r	Controls the rate of exponential decay to control edge distance in impact score calculation.  Default: 0.25
+**-r**	Controls the rate of exponential decay to control edge distance in impact score calculation.  Default: 0.25
 
--perm	Sets the number of permutations for p-value calculations.  Default: 10000
+**-perm**	Sets the number of permutations for p-value calculations.  Default: 10000
 
--rstate	Sets the random state for reproducible results.  Default: Current Time (milliseconds)
+**-rstate**	Sets the random state for reproducible results.  Default: Current Time (milliseconds)
 
--refflat	Specifies the UCSC refflat file to use to identify TSS locations of genes in pathways. Required for identifying non-coding regulators. Gene identifiers will need to match those provided in the expression file.
+**-refflat**	Specifies the UCSC refflat file to use to identify TSS locations of genes in pathways. Required for identifying non-coding regulators. Gene identifiers will need to match those provided in the expression file.
 
--ci	Sets the tab-delimited file for chromatin interaction data to identify non-coding targets of genes
+**-ci**	Sets the tab-delimited file for chromatin interaction data to identify non-coding targets of genes
 
--nct	Sets the bed file for non-coding targets to be associated with genes. If chromatin interactions are provided these sites will be connected via chromatin interactions, otherwise it will be proximity based
+**-nct**	Sets the bed file for non-coding targets to be associated with genes. If chromatin interactions are provided these sites will be connected via chromatin interactions, otherwise it will be proximity based
 
--proxSets the proximity based non-coding target threshold which spans the base pair distance both upstream and downstream from the transcription start site.  Default: 50000
+**-prox**	Sets the proximity based non-coding target threshold which spans the base pair distance both upstream and downstream from the transcription start site.  Default: 50000