CHANGES IN VERSION 1.1.6 ------------------------ NEW FEATURES o Added DNAcopy algorithm to Strand-seq mode. SIGNIFICANT USER-LEVEL CHANGES o Renamed parameter 'most.frequent.state.bivariate' -> 'most.frequent.state.strandseq'. o Renamed parameter 'most.frequent.state.univariate' -> 'most.frequent.state'. o New parameter 'strandseq'. BUG FIXES o Dendrogram and heatmap are now aligned properly in heatmapGenomewide(). CHANGES IN VERSION 1.1.5 ------------------------ NEW FEATURES o Aneufinder runs DNAcopy algorithm in addition to the Hidden Markov Model. o New function "getQC" to get a data.frame with quality metrics. SIGNIFICANT USER-LEVEL CHANGES o Changed folder structure to include DNAcopy method. o Renamed methods from c('univariate','bivariate') to c('HMM','biHMM') CHANGES IN VERSION 1.1.4 ------------------------ NEW FEATURES o karyotypeMeasures() has new option regions. o plotHeterogeneity() for easy plotting of karyotype measures. o BiocStyle vignette. o New option use.bamsignals=FALSE/TRUE available for the binning step. o getQC() handles NULL entries as NA and is thus more robust. o complexity estimation via Michaelis-Menten is carried along. SIGNIFICANT USER-LEVEL CHANGES o Color scheme for copy number states has been improved for states >= 5-somy. o Option format has been removed in all functions. File format is determined automatically now. o clusterByQuality() clusters now on complexity as well by default. DEPRECATED AND DEFUNCT BUG FIXES o Corrected bug in order of seqlevels after as(..., 'GRanges'). o Corrected bug in hotspotter() that caused detection of low-abundance hotspots.