Changes in version 1.2.4 (2015-01-21)
-------------------------------------

OTHER

    o update package maintainer

Changes in version 1.2.3 (2015-01-20)
-------------------------------------

BUG FIXES

    o createBins() now also works for species not supported by GenomeInfoDb
      (such as Canis lupus familiaris)

Changes in version 1.2.2 (2014-12-23)
-------------------------------------

IMPROVEMENTS

    o applyFilters() now ignores the residual filter for chromosomes for which
      it does not exist (instead of always filtering out the entire chromosome)

Changes in version 1.2.1 (2014-11-01)
-------------------------------------

IMPROVEMENTS

    o add an asterisk in the noise measure to clarify it's not a regular
      standard deviation or variance, but first scaled with the mean (so that
      the mean is 1.0 and the relationship holds between variance and 1/N, where
      N is the average number of reads per bins)

    o clarify the use of log2/sqrt transformation in segmentBins()

Changes in version 1.2.0 (2014-10-14)
-------------------------------------

RELEASE

    o Bioconductor 3.0

IMPROVEMENTS

    o segmentBins() supports another transformation option besides log2:
      sqrt(x + 3/8), which stabilizes the variance

    o plot() can skip plotting of segments and calls by specifying
      doSegments=FALSE and doCalls=FALSE

    o exportBins() also supports BED files

BUG FIXES

    o exportBins() saves base pair positions in fixed notation instead of
      scientific

Changes in version 1.0.5 (2014-06-13)
-------------------------------------

BUG FIXES

    o fix a bug caused by package matrixStats changing madDiff() from an S4
      to an S3 method in version 0.9.4, released on 2014-05-23

Changes in version 1.0.4 (2014-05-23)
-------------------------------------

BUG FIXES

    o getBinAnnotations() fixed after being broken by a change in Bitbucket

Changes in version 1.0.3 (2014-05-23)
-------------------------------------

IMPROVEMENTS

    o added exportBins() for exporting to a file

    o switch graphics in the vignette to PNG

Changes in version 1.0.2 (2014-05-15)
-------------------------------------

IMPROVEMENTS

    o plot() honors user-specified values for xlab and xaxt

    o plot() allows omission of labels for the standard deviation and
      the number of data points

    o improve diagnostic messages

Changes in version 1.0.1 (2014-04-17)
-------------------------------------

BUG FIXES

    o smoothOutlierBins() correctly ignores bins filtered out

Changes in version 1.0.0 (2014-04-14)
-------------------------------------

RELEASE

    o initial release as part of Bioconductor 2.14
