new for version 1.19.1 ====================== * Addresed an error in one of the internal functions fitting the null model distribution generated by the new way NAs are treated in R3.5.0+ lm() function new for version 1.9.5 ===================== * metaVIPER analysis was implemented in the viper function. It can be invoked by simply passing a list of regulons objects to the regulon parameter in the viper function. * To improve stability of p-value estimations with sample permutations, a normal distribution for the ES is assumed when less than 500 permutations are provided for the NULL model. new for version 1.5.5 ===================== Example code was modified to reduce computation time new for version 1.5.4 ===================== Added the argument processAll to msviperCombinatorial that allow the evaluation of synergy between pairs showing enrichment not significantly higher than the singe regulons new for version 1.5.3 ===================== New implementation of the aREA algorithm allowing for missing values and weighting the contribution of each datapoint in the expression matrix and new for version 1.5.2 ===================== New function aracne2regulon4cnv to parse ARACNe results generated by using different expression files for regulators and targets new for version 1.5.1 ===================== Bug fixed in aracne2regulon function new for version 1.3.2 ===================== Added function msviperClass ro generate instances of the msviper class new for version 1.3.1 ===================== Use of multiple cores based on the parallel package new for version 1.1.0 ===================== A bug in aracne2regulon function related to collapsing the regulons at the gene level was fixed A bug in the aecdf function was fixed Implemented a new pleiotropy algorithm aREA function was rewritten with improved performance Computation of empirical p-values was performed assuming a symmetric distribution of the ES around 0 for the NULL model, increasing in this way the power of the test by a factor of 2 A function to compute the similarity between VIPER signatures (viperSimilarity) was added to the package new for version 0.99.1 ====================== Bug fixed in shadow() function that was crashing when one regulon was completely contained into another regulon.