CHANGES IN VERSION 1.11.6
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Changed the default style to BiocStyle::html_document to mirror recent
        changes in BiocStyle.


CHANGES IN VERSION 1.11.4
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Vignette now uses the new BiocStyle::html_document that was recently
        released.


CHANGES IN VERSION 1.11.2
-------------------------

BUG FIXES

    o Fixed the citations.
    o Fixed DESeq2Report() for limma-results so that it will properly cite
        limma.

CHANGES IN VERSION 1.11.1
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o DESeq2Report() can now be used with other software if their results are
         made to look like DESeq2 results. For example, with limma-voom results.
         
BUG FIXES

    o Made the DESeq2Report() more robust in case rlog() fails initially.


CHANGES IN VERSION 1.9.1
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Changed the default style to BiocStyle::html_document2.

CHANGES IN VERSION 1.7.10
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Help pages now document advanced arguments.

CHANGES IN VERSION 1.7.2
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Dropped defunct functions.


CHANGES IN VERSION 1.5.48
-------------------------

BUG FIXES

    o Fixed a bug in derfinderReport() for a case when there are significant
        regions but not all regions have finite areas.

CHANGES IN VERSION 1.5.43
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o edgeReport() now includes two edgeR specific plots: one showing the BCV
        and another showing a 2-dim MDS. Also added more edgeR citations that I
        missed earlier: thank you Gordon Smyth!

CHANGES IN VERSION 1.5.33
-------------------------

NEW FEATURES

    o Added the function edgeReport() for creating HTML or PDF reports based on
        edgeR results. Together with DESeq2Report() now regionReport supports
        the two most used packages for RNA-seq feature-level analysis.


CHANGES IN VERSION 1.5.19
-------------------------

NEW FEATURES

    o Added the templates 'templatePvalueHistogram' and 'templateHistogram'
        to be used with renderReport() if you prefer histogram plots instead
        of density plots.

CHANGES IN VERSION 1.5.12
-------------------------

NEW FEATURES

    o Added the function DESeq2Report() for creating HTML or PDF reports based
        on DESeq2 results. This should also be useful to explore derfinder
        results created from the expressed regions-level approach.

SIGNIFICANT USER-VISIBLE CHANGES

    o Added a 'digits' argument to control how to round some numerical variables
        in all type of reports.
    o Added a 'theme' argument to allow setting the ggplot2 theme for the plots.
    
BUG FIXES

    o Improved the PDF versions of all reports by hiding code and shortening
        tables. Also added a warning to switch the device to 'pdf' for PDF
        output since it looks better than the default 'png'.

CHANGES IN VERSION 1.5.6
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Switched to using rmarkdown instead of knitrBootstrap as the default
        engine for creating the reports.

CHANGES IN VERSION 1.3.8
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o renderReport() and derfinderReport() now show Manhattan plots for p-value
        variables (p-value, q-value, FWER adjusted p-value).


CHANGES IN VERSION 1.3.7
------------------------

NEW FEATURES

    o renderReport() now has the 'densityTemplates' argument via which users can
        customize the density plots for the p-value variables and the continuous
        variables. This addresses one of David Robinson's requests at
        http://f1000research.com/articles/4-105/v1



CHANGES IN VERSION 1.3.6
------------------------

NEW FEATURES

    o Added a vignette with an example report from bumphunter results.

CHANGES IN VERSION 1.3.5
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Merged pull request https://github.com/leekgroup/regionReport/pull/7
    o Added "template" argument to renderReport and derfinderReport to
        customize the knitr template used
    o Wrapped code that works in a temporary directory in with_wd function, 
        which evaluates in the directory but returns to the original directory 
        in the case of a user interrupt or error (with on.exit)
    


CHANGES IN VERSION 1.3.4
------------------------

NEW FEATURES

    o Reports now have a link to the BibTeX file used for the references. This
        addresses http://f1000research.com/articles/4-105/v1#reflist Karthik
        Ram's bullet point number 4.

CHANGES IN VERSION 1.3.3
------------------------

NEW FEATURES

    o Now uses derfinderPlot::vennRegions() to show venn diagram of genomic
        states. Requires derfinderPlot version 1.3.2 or greater.
    o derfinderReport() now has a 'significantVar' argument that allows users to
        choose between determining significant regions by P-values, FDR adjusted
        P-values, or FWER adjusted P-values (if FWER adjusted P-values are
        absent, then FDR adjusted P-values are used instead, with a warning).


CHANGES IN VERSION 1.3.2
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Deprecated functions with underscores in their names in favor of 
        camelCase functions. This was done to simplify the package.

CHANGES IN VERSION 1.3.1
------------------------

BUG FIXES

    o Fixed renderReport() and derfinderReport() so they'll open the correct URL
        when interactive() == TRUE and the user has knitrBootstrap version 0.9.0
        installed instead of the latest GitHub version.


CHANGES IN VERSION 1.1.9
------------------------

NEW FEATURES

    o Introduced renderReport() which creates a simple exploratory report for
        any set of genomic regions. It allows the user to further customize the
        report by using a child file.
    o You can now use the 'output_format' advanced parameter on both 
        renderReport() and derfinderReport() to output a PDF file instead
        of an HTML file. The interactive tables are lost and only the top 20
        rows are shown.

CHANGES IN VERSION 1.1.8
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Adapted to work with bumphunter >= 1.7.6


CHANGES IN VERSION 1.1.7
------------------------

NEW FEATURES

    o Users can now control 'output_format' and 'clean' options from
        rmarkdown::render() when running derfinderReport()


CHANGES IN VERSION 1.1.3
------------------------

BUG FIXES

    o Adapted derfinderReport() to derfinder 1.1.5


CHANGES IN VERSION 0.99.0
-------------------------

NEW FEATURES

    o Preparing to submit to Bioconductor.

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated the vignette and the package to work with recent versions of
        the packages this package depends on.
    o Renamed the package from derfinderReport to regionReport and
        generateReport() to derfinderReport(). In the future we will add
        another report for a general GRanges object.
    o Simplified derfinderReport()'s call by using advanced arguments.
    o Added Travis integration.


CHANGES IN VERSION 0.0.18
-------------------------

    o Now derfinderReport() has a 'chrsStyle' argument to match changes in 
    derfinder version 0.0.60. 'chrsStyle' is set to 'UCSC' by default.

CHANGES IN VERSION 0.0.17
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Made more robust for cases where there is a small number of significant
        DERs: need at least 3 observations by chr for the chr to be included in
        the density plots.

CHANGES IN VERSION 0.0.16
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o MA-style plots now use the scaling factor.
    o Using a GAM smoother instead of loess for MA-style plots. Helps for cases
        with many regions.

CHANGES IN VERSION 0.0.13
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added a vignette

CHANGES IN VERSION 0.0.12
-------------------------

BUG FIXES

    o complying with BiocCheck version 1.0.0

CHANGES IN VERSION 0.0.11
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o genomicState data moved to derfinder 0.0.53

CHANGES IN VERSION 0.0.8
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Now requires knitrBootstrap 1.0.0
    o Matches derfinder version 0.0.49

CHANGES IN VERSION 0.0.3
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Matches derfinder version 0.0.34

CHANGES IN VERSION 0.0.1
-----------------------

NEW FEATURES

    o Migrated from derfinder
