v1.1.5
	Bugfixes:
		- Fixed minor bug in database setup that caused instability with cuffdiff --no-diff argument.
		- Fixed bug in csDendro method for CuffData objects.

v1.1.4
	New Features:
		- Added MAplot() method to CuffData objects.
	Bugfixes:
		- Finished abrupt migration to reshape2. As a result fixed a bug in which 'cast' was still required for several functions and could not be found. Now appropriately using 'dcast' or 'acast'.
		- Fixed minor bug in CuffFeature::fpkmMatrix
		
v1.1.3 
	New Features:
		- getSig() has been split into two functions: getSig() now returns a vector of ids (no longer a list of vectors), and getSigTable() returns a 'testTable' of 
		binary values indicating whether or not a gene was significant
		in a particular comparison.
		- Added ability in getSig() to limit retrieval of significant genes to two provided conditions (arguments x & y). (reduces time for function call if you have a specific comparison in mind a priori)
			* When you specify x & y with getSig(), q-values are recalculated from just those selected tests to reduce impact of multiple testing correction.
			* If you do not specificy x & y getSig() will return a vector of tracking_ids for all comparisons (with appropriate MTC). 
		- You can now specify an 'alpha' for getSig() and getSigTable() [ 0.05 by default to match cuffdiff default ] by which to filter the resulting significance calls.
		- Added csSpecificity() method:  This method returns a feature-X-condition matrix (same shape as fpkmMatrix) that provides a 'condition-specificity' score  
			* defined as 1-(JSdist(p,q))
			  where p is is the density of expression (probability vector of log(FPKM+1)) of a given gene across all conditions, 
			  and q is the unit vector for that condition (ie. perfect expression in that particular condition)
			* specificity = 1.0 if the feature is expressed exclusively in that condition
		- Created csDendro() method: This method returns a object of class 'dendrogram' (and plots using grid) of JS distances between conditions for all genes in a CuffData, CuffGeneSet, or CuffFeatureSet object.
			* Useful for identifying relationships between conditions for subsets of features
		- New visual cues in several plot types that indicates the quantification status ('quant_stat' field) of a particular gene:condition. This information is useful to indicate whether or not
		to trust the expression values for a given gene under a specific condition, and may provide insight into outlier expression values.
			* This feature can be disabled by setting showStatus=F.
		- csDensity() is now available for CuffFeatureSet and CuffGeneSet objects
	
	Bugfixes:
		- Fixed bug in getGenes that may have resulted in long query lag for retrieving promoter diffData. As a result all calls to getGenes should be significanly faster.
		- CuffData fpkm argument 'features' now returns appropriate data.frame (includes previously un-reported data fields).
		- Replaced all instances of 'ln_fold_change' with the actual 'log2_fold_change'.  Values were previously log2 fold change but database headers were not updated to reflect this.
		- Fixed bug that could cause readCufflinks() to die with error when using reshape2::melt instead of reshape::melt.
	
	Notes:
		- ***The structure of the underlying database has changed in this version.  As a consequence, you must rebuild you cuffData.db file to use new version. readCufflinks(rebuild=T)***
		- Updated vignette
		- A 'fullnames' logical argument was added to fpkmMatrix. If True, rownames for fpkmMatrix will be a concatenation of gene_short_name and tracking_id.
		This has the added benefit of making row labels in csHeatmap easier to read, as well as preserving uniqueness. 
		- Slight speed improvements to JSdist (noticeable when using csCluster on large feature sets).
		- 'testTable' argument to getSig() has been dropped in lieu of new getSigTable() method.
	
v1.1.1
	Bugfixes:
		- fixed issue in which there was no graceful error handling of missing CDS or TSS data in cuffdiff output.
		- Fixed issue in which distribution test data (promoters, splicing, relCDS) were not appropriately added to objects on creation.
		- Fixed bug that would sometimes cause csBoxplot() to throw an error when log-transforming fpkm data. Also added pseudocount argument.
		- Fixed bug that would cause diffData() to return a filtered subset of results by default.
		- Adjusted indexing of tables to improve performance on large datasets.
		- Fixed bug that caused diffData method to not be registered with CuffFeature and CuffGene objects.
		- Fixed bug that sometimes caused over-plotting of axis labels in csBarplots.  
		
	New Features:	
		- added getSig method to CuffSet class for rapid retrieval of significant features from all pairwise tests (as a list of IDs). 
		By default the level is 'genes' but any feature level can be queried.
		- csCluster now uses Jensen-Shannon distance by default (as opposed to Euclidean)
		- Added 'xlimits' argument to csVolcano to constrain plot dimensions.
		- Enforced requirement in csVolcano for x and y arguments (as sample names).
	
	Notes:
		- Changed dependency 'reshape' to 'reshape2'
		- Changed the default orientation of expressionBarplot() for CuffFeatureSet objects.
		- Changed output of csCluster to a list format that includes clustering information. As a result, I created the function csClusterPlot
		to replace the previous default drawing behavior of csCluster.  This allows for stable cluster analysis.
		- For consistency, the 'testId' slot for CuffDist objects was renamed to 'idField'.  This brings the CuffDist class in line with the CuffData class.
		- CuffGene and CuffGeneSet now include slots for promoter, splicing, and relCDS distribution test results.
v1.0.0
	- Official public release. No changes from v0.99.5

v0.99.5
	- Significant speed improvements to readCufflinks() for large cuffdiff datasets.
		- Tables written first then indexed.
	- Added slot accessor methods to avoid using slots directly.
	
v0.99.4
	- Second beta release and submission to Bioconductor

v0.1.3 Release 2011-08-18:
	- First Beta release of cummeRbund and submission to Bioconductor for review and hosting.