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