Changes in version 1.4.2 (2015-08-20)
-------------------------------------

BUG FIXES

    o createBins() now properly selects chromosomes when ignoring 
      mitochondrial DNA. Please note that the mitochondrial DNA is only 
      effectively ignored when it is in the form "chrM" or "M".

Changes in version 1.4.1 (2015-06-30)
-------------------------------------

IMPROVEMENTS

    o correctBins() now filters out bins with missing loess correction estimate

Changes in version 1.4.0 (2015-04-17)
-------------------------------------

RELEASE

    o Bioconductor 3.1

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
