Changes in version 2.4.1: BUG FIXES o Fixed the warning due to the changes of Rcpp package. Changes in version 1.99.4: SIGNIFICANT USER-VISIBLE CHANGES o Typos in the vignette are fixed. Changes in version 1.99.3: BUG FIXES o mosaicsFit(): mismatch between function and help fixed. Changes in version 1.99.2: SIGNIFICANT USER-VISIBLE CHANGES o mosaicsFit(): Sets bgEst="rMOM" as default. o Help documents are polished and updated. o Vignette is updated. Changes in version 1.99.1: SIGNIFICANT USER-VISIBLE CHANGES o mosaicsFitHMM() & mosaicsPeakHMM(): Hidden-Markov-Model-based MOSAiCS model fitting & peak calling, respectively, to identify broad peaks such as histone modifications. o Add new class 'MosaicsHMM' with methods show(), plot(), & estimates(). o mosaicsFit(): Introduces a new argument 'trans'. o mosaicsFit(): Stability & robustness of model fitting were improved. o Polish help documents of constructBins(), generateWig(), and mosaicsRunAll(). o Tested to work with >= R 3.0 properly. BUG FIXES o constructBins() & export(): Use correct base for BED file (one base shift). o Reflect the changes in Rcpp packages that mosaics package depends on. Changes in version 1.5.3: BUG FIXES o mosaicsRunAll(): Bug fix when byChr = TRUE. Changes in version 1.5.2: SIGNIFICANT USER-VISIBLE CHANGES o constructBins(): Supports aligned read file formats for PET data (eland results and SAM formats). o mosaicsRunAll(): Supports aligned read file formats for PET data. o Add generateWig(): Constructs wiggle files for PET and SET data. o Use tab separator instead of whitespaces for generateWig() and constructBins(). o Improve the vignette (case studies, example lines for input files, generateWig()). BUG FIXES o constructBins(): Bug fix for capping and excludeChr. Fix incorrect summary when byChr = TRUE. o mosaicsRunAll(): Bug fix for excludeChr & handling the full path for chipFile and controlFile. Changes in version 1.5.1: SIGNIFICANT USER-VISIBLE CHANGES o constructBins(): Chromosome information can now be specified. o mosaicsRunAll(): Chromosome information can now be specified. Changes in version 1.4.1: BUG FIXES o constructBins(): Bug fix for the "outfileLoc" argument. o mosaicsFit(): Minor changes in two-signal-component model fitting. o mosaicsPeak(): No warning with the updated IRanges package. Changes in version 1.4.0: o BioConductor release 2.10. Changes in version 1.3.4: SIGNIFICANT USER-VISIBLE CHANGES o Improve help documents for all classes and functions. BUG FIXES o mosaicsPeak(): Correct bin size calculation when binsize=NA. Changes in version 1.3.2: SIGNIFICANT USER-VISIBLE CHANGES o Simplify arguments of mosaicsRunAll(), constructBind(), and export(). o Add parallel argument in mosaicsFit(). o Extensive use of parallel processing/computing. o Overall speed improvements in the package. o Update the vignette. o Use parallel package instead of multicore package. 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).