
CHANGES IN VERSION 1.3.9
--------------------------
BUG FIXES

     o Dependency GOSeq 1.23.2 no longer supports gene ID system "refGene", so it has been changed to Entrez Gene IDs under the name "knownGene" instead. Merged gene tables now key off ENTREZ instead of REFSEQ. Now tested and built on R 3.3.0. 


CHANGES IN VERSION 1.3.8
--------------------------
FEATURE

     o Adjusting the color thresholds for HMG diagram and Gamma scores to be properly scaled by dimensionality. Previous z-scoring method was occasionally making errors. Now a Gamma score of 1 indicates the distance between centroids, which would otherwise naturally scale by the square root of the geneset dimension. 
     o Updated Vignette


CHANGES IN VERSION 1.3.6
--------------------------
FEATURE

     o Simplified final output figure "HMG" and associated tables "HMG1" and "HMG2" calculate the distance to each centroid so the interpretation of results is simpler. Strong overlap to the HMA file.
     o Entries in the Vignette for this new 2 table output. 



CHANGES IN VERSION 1.3.4
--------------------------
BUG FIXES

     o Dependency GenomicRanges no longer exports "assay()" 


CHANGES IN VERSION 1.3.3
--------------------------
Rebuilt for R 3.2.2
BUG FIXES

     o Biomart.org went down for "ensembl" late 2015. now we ask "www.ensembl.org" directly for their mart. Resolves some warnings, and fixes ID collection.

CHANGES IN VERSION 0.99.15
--------------------------

BUG FIXES

     o bugfix in gene ID systems passed to goseq. 

CHANGES IN VERSION 0.99.12
--------------------------

NEW FEATURES

     o expanding user manuals to clarify how figures and clustering is performed. 


CHANGES IN VERSION 0.99.11
---------------------------

BUG FIXES

     o bugfix in ProcessAll cardinality message. 
     o Error catching around PCA. 
     o Heatmap genelist now respects Annote_Filter file when LIMIT$HARD. 
     o Cleaned up warnings when no rows for HMA. 
     o Bugfix in PCA regarding non-negative definite covariance from princomp's eigen: replaced all instances with prcomp(). 

CHANGES IN VERSION 0.99.10
--------------------------

BUG FIXES

     o  bugfix in G$LIMIT$baseMean and explanations of naming conventions in the vignette.

CHANGES IN VERSION 0.99.4
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

     o replacing DESeq with DESeq2 Fall2014

CHANGES IN VERSION 0.0.0
------------------------

NEW FEATURES

     o Release package. Fall 2014.
