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.