
CHANGES IN VERSION 1.11.7
--------------------------

USER-LEVEL CHANGES

	o simplify functions 'get_expression' and 'plot_expression'
	  (remove option to automatically use data from last aba_enrich-call)
	o 'plot_expression' now takes matrix from 'get_expression' as input,
	  instead of calling 'get_expression' internally
	o add color key to 'plot_expression' heatmap when gene-associated
	  variables are shown in a colored side bar


CHANGES IN VERSION 1.11.6
--------------------------

USER-LEVEL CHANGES

	o sort output aba_enrich()[[1]] by FWER first and then by age category
	  (previously it was sorted by age category first)
	  


CHANGES IN VERSION 1.11.3
--------------------------

	o remove all C++ code and depend on package
	  GOfuncR instead


CHANGES IN VERSION 1.11.2
--------------------------

USER-LEVEL CHANGES

	o when coordinates are used,
	  remove genes with multiple gene-coordinates
	  (coordinates are used when the familiy-wise error rate is
	  corrected for gene length or spatial clustering of genes)
	  
	  
CHANGES IN VERSION 1.11.1
--------------------------

NEW FEATURES

	o allow for custom gene-coordinates
	  (alternative to integrated coordinates;
	  coordinates are used when the familiy-wise error rate is
	  corrected for gene length or spatial clustering of genes)


CHANGES IN VERSION 1.8.0
------------------------

NEW FEATURES
	  
	o two new statistical tests are available
	  (in addition to hypergeometric and Wilcoxon rank-sum test):
	  1) binomial test when genes are associated with two counts
		 (e.g. number of amino-acid changes in two species 
		 since a common ancestor);
	  2) 2x2 contingency table test when genes are associated with
		 with four counts (e.g. number of non-synonymous or synonymous 
		 variants that are fixed between or variable within species.)
	o new 'silent' option represses all output to the screen
	  except for warnings and error messages


USER-LEVEL CHANGES

	o default 'genes' input is now a dataframe with 
	  gene-identifiers in column 1 and gene-associated variables,
	  like scores or counts in the other columns
	  (the old vector-input will still work
	  for hypergeometric and Wilcxon rank-sum test)
	o sort aba_enrich(...)[[1]] output also on structure-ID
	  (after sorting on age category and FWER)
	o sort genes in 'get_annotated_genes' output (mixedsort)
	o rename aba_enrich() column 'times_FWER_under_0.05' to 'n_significant'

IMPROVEMENTS
	  
	o performance improvements for aba_enrich and
	  get_annotated_genes
	o modified generation of temporary files allows 
	  parallel processing with mclapply


