
CHANGES IN VERSION 1.11.1
------------------------


    o Fixed a bug in EBTest() which may cause error when performing isoform DE testing 1 sample vs. multiple samples.

CHANGES IN VERSION 1.9.3
------------------------


    o Correct typos in GetDEResults help file.
    o Include an alternative method for normalization. The alternative method is similar to median-by-ratio normalization, 
    	but can deal with the cases when all of the genes/isoforms have at least one zero counts (in which case the 
    	median-by-ratio normalization will fail). This alternative method is developed for single-cell RNA-seq analysis
    	where the dataset always contains a large amount of zeros.
	
CHANGES IN VERSION 1.9.2
------------------------


    o Fixed a bug which may cause error when input a matrix to the sizeFactors parameter
	
CHANGES IN VERSION 1.9.1
------------------------


    o Added Q&A seqction in vignette to address common questions
	
CHANGES IN VERSION 1.7.1
------------------------


    o In EBSeq 1.7.1, EBSeq incorporates a new function
		GetDEResults() which may be used to obtain a list of transcripts under a target FDR
		in a two-condition experiment.
		The results obtained by applying this function with its default setting will be
		more robust to transcripts with low variance and potential outliers.
		By using the default settings in this function,
		the number of genes identified in any given analysis may
		differ slightly from the previous version (1.7.0 or order). 
		To obtain results that are comparable
		to results from earlier versions of EBSeq (1.7.0 or older), a user may set
		Method="classic" in GetDEResults() function, or use the original GetPPMat() function.
		The GeneDEResults() function also allows a user to modify thresholds to
		target genes/isoforms with a pre-specified posterior fold change.

    o Also, in EBSeq 1.7.1, the default settings in EBTest() and EBMultiTest() function 
		will only remove transcripts with all 0's (instead of removing transcripts with 
		75th quantile less than 10 in version 1.3.3-1.7.0). 
		To obtain a list of transcripts comparable to the results generated by 
		EBSeq version 1.3.3-1.7.0, a user may change Qtrm = 0.75 and QtrmCut = 10
		when applying EBTest() or EBMultiTest() function.


CHANGES IN VERSION 1.5.4
------------------------


    o An extra numerical approximation step is implemented 
    in EBMultiTest() function to avoid
    underflow. The underflow is likely due to large number of samples.
    A bug in EBMultiTest() is fixed. The bug will cause error when there is
    exactly 1 gene/isoform that needs numerical approximation.

CHANGES IN VERSION 1.5.3
-------------------------

BUG FIXES

    o Fixed a bug that may generate NA FC estimates when there are no replicates.

CHANGES IN VERSION 1.5.2
------------------------

NEW FEATURES

    o An extra numerical approximation step is 
    implemented in EBTest() function to avoid
    underflow. The underflow is likely due to large number of samples.


CHANGES IN VERSION 1.3.3
------------------------

NEW FEATURES

    o In EBSeq 1.3.3, the default setting of EBTest function will remove 
    low expressed genes (genes whose 75th quantile of normalized counts is less 
    than 10) before identifying DE genes. 
    These two thresholds can be changed in EBTest function.
		Because low expressed genes are disproportionately noisy, 
		removing these genes prior to downstream analyses can improve model fitting and increase robustness
		(e.g. by removing outliers).

