Changes in version 1.2.5: o Correct version number in DESCRIPTION and package?mosaics. Changes in version 1.2.4: SIGNIFICANT USER-VISIBLE CHANGES o Add parallel argument in readBins(). o Add parallel argument in mosaicsRunAll(). BUG FIXES o DESCRIPTION: 'multicore' package in 'Enhances' instead of 'Suggests'. Changes in version 1.2.3: NEW FEATURES o New model for deeply sequenced ChIP-seq data. o Genome-wide analysis of ChIP-seq data is now available. o Supports more aligned read file formats: eland_result, eland_extended, eland_export, bowtie, SAM, BED, CSEM. o Preprocessing of aligned read files can be done within the R environment using constructBins(). o Easier model fitting for the two sample analysis using mosaicsRunAll(). o Preprocessing and model fitting become much faster (Rcpp). o Parallel processing/computing is now supported (multicore). SIGNIFICANT USER-VISIBLE CHANGES o Add constructBins(): Preprocess aligned read files to bin-level files. o Add mosaicsRunAll(): Convenient two sample analysis. o Add bgEst argument in mosaicsFit(): Choose background estimation approach. o Add nCore argument in readBins(): Parallel processing. o Vignettes is now extensively updated. o Rcpp package is required and multicore package is suggested. DEPRECATED AND DEFUNCT o Drop chrID argument in export(). BUG FIXES o Fix mosaicsPeak() for the case that no peak is called. o Fix export() by removing unnecessary spaces in output text files. Changes in version 1.2.0: o BioConductor release 2.9. Changes in version 1.0.1: o Fixes for 'plot' method of class 'binData'. Changes in version 1.0.0: o On BioConductor (release 2.8).