Changes in version 1.5.10:

    o   Restored normalize() as a S4 method returning a
	 RangedSummarizedExperiment object.

    o   Modified asDGEList() to use any available normalization data in the
	 input object.

    o   Generalized S4 methods to apply on SummarizedExperiment objects.

    o   Removed the rescue.ext option for PE handling, to maintain
	 consistent totals calculations.

    o   Removed the fast.pe option for PE data handling, in favour of
	 improved default processing.

    o   Removed dumpPE(), which is not required without the fast.pe option.

    o   Removed makeExtVector() in favour of list/DataFrame specification.

    o   windowCounts() and regionCounts() now compute and store the mean PE
	 size and read length.

    o   Minor fix in correlateReads() for end-of-chromosome behaviour.

    o   Modified checkBimodality() so that the width argument behaves like
	 ext in windowCounts().

    o   extractReads() with as.reads=TRUE for PE data now returns a
	 GRangesList.

    o   Added the controlClusterFDR(), clusterWindows() and
	 consolidateClusters() functions to automate control of the
	 cluster-level FDR.

    o   Added protection against NA values in the cluster IDs for
	 combineTests(), getBestTest(), upweightSummits().

    o   All read extraction methods are now CIGAR-aware and will ignore
	 soft-clipped parts of the alignment.

Changes in version 1.4.0:

    o   Added clusterFDR() function to compute the FDR for clusters of DB
	 windows.

    o   Added checkBimodality() function to compute bimodality scores for
	 regions.

    o   Modified normalize(), asDGEList() to allow manual specification of
	 library sizes.

    o   Switched from normalizeCounts(), normalize() to S4 method
	 normOffsets().

    o   Modified default parameter specification in strandedCounts(), to
	 avoid errors.

    o   Switched to warning from error when a restricted chromosome is
	 specified in extractReads().

    o   Modified extractReads() interface with improved support for extended
	 read and paired read extraction.

    o   Added normalization options to filterWindows() when using control
	 samples.

    o   Fixed bug for proportional filtering in filterWindows().

    o   Allowed correlateReads() to accept paired-end specification when
	 extracting data.

    o   Added maximizeCcf() function to estimate the average fragment
	 length.

    o   Added support for strand-specific overlapping in detailRanges().

    o   Increased the fidelity of retained information in dumped BAM file
	 from dumpPE().

    o   Modified strand specification arguments for profileSites(), allowed
	 reporting of individual profiles.

    o   Removed param= specification from wwhm().

    o   Switched to RangedSummarizedExperiment conventions for all relevant
	 functions.

    o   Switched to mapqFilter for scanBam() when filtering on mapping
	 quality.

    o   Added tests for previously untested functions.

    o   Slight updates to documentation, user's guide.

Changes in version 1.2.0:

    o   Added getWidths(), scaledAverage() and filterWindows(), to
	 facilitate comparison of abundances during filtering.

    o   Added findMaxima() to identify locally maximal windows from range
	 data.

    o   Added profileSites() to examine the coverage profile around
	 specified regions, with wwhm() to guess the ideal window size from
	 the profile.

    o   Changed default window width in windowCounts() to 50 bp, default
	 filter to a fixed count of 10. Also, filter=0 is honored when
	 bin=TRUE.

    o   Switched from the depracated rowData to rowRanges for all
	 manipulations of SummarizedExperiment.

    o   Changed all instances of `pet' to `pe' in read parameter
	 specification, and renamed getPETSizes() to getPESizes().

    o   Removed the redundant rescue.pairs parameter in readParam().

    o   Added fast.pe parameter in readParam(), for fast paired-end data
	 extraction. Added dumpPE() to pre-process paired-end BAM files for
	 fast downstream extraction.

    o   Added support for custom column specification in getBestTest(),
	 combineTests().

    o   Switched from reporting average log-FC to numbers of up/down windows
	 in combineTests().

    o   Allowed getBestTest() to return all fields associated with the best
	 window in the output table.

    o   Added upweightSummits() to compute weights favouring high-abundance
	 windows.

    o   Added combineOverlaps(), getBestOverlaps() and summitOverlaps()
	 wrapper functions for processing of Hits objects.

    o   Added consolidateSizes(), to consolidate DB results from multiple
	 window sizes.

    o   Added support for custom key/name specification in detailRanges()
	 for non-human/mouse systems.

    o   Added support for strand-specific read extraction in readParam(),
	 strand-specific counting via strandedCounts().

    o   Added strand-awareness to mergeWindows(). Added protection against
	 stranded input regions in extractReads(), detailRanges().

    o   Changed algorithm for splitting of large peaks in mergeWindows().

    o   Stored counting parameters in exptData for windowCounts(),
	 regionCounts().

    o   Fixed small inaccuracies with continuity correction addition in
	 normalizeCounts() for NB-loess.

    o   Switched to fragment midpoint for binning of paired-end data in
	 windowCounts().

    o   Added support for lists of library-specific readParam objects in
	 windowCounts(), regionCounts(), correlateReads().

    o   Added makeExtVector(), to support variable read extension lengths
	 between libraries in windowCounts(), regionCounts().

    o   Added support for read extension within extractReads().

    o   Updated the user's guide to reflect new and modified functions.

    o   Added sra2bam.sh in inst/doc to reproducibly generate BAM files to
	 run UG examples.

    o   Cleaned up code in inst/tests for modified functions, added new
	 tests for new functions.

Changes in version 1.0.0:

    o   New package csaw, for de novo detection of differential binding in
	 ChIP-seq data.