Changes in version 1.1.2                        

  - minor fix in doc for preparePlotgardener

                        Changes in version 1.1.1                        

  - HicAggR is now on bioconductor release 3_19
  - added a minor fix to ExtractSubmatrix when using GRanges object to
    extract, retain only GRanges with seqnames that are present in
    hicList
  - added preparePlotgardener function to generate a data.frame that can
    be directly used in plotgardener's plotHicTriangle, plotHicRectangle
    and plotHicSquare directly

                       Changes in version 0.99.7                        

  - caching in vignette

                       Changes in version 0.99.6                        

  - default set column names in OrientateMatrix are now removed, this is
    for ggAPA
  - ggAPA: "rf" mode has it's own customized axes labels now
  - added introduction to the package's vignette

                       Changes in version 0.99.5                        

  - added option to remove duplicated submatrices in SearchPairs

                       Changes in version 0.99.4                        

  - removed CITATION file

                       Changes in version 0.99.3                        

  - NAMESPACE was generated with roxygen2 to define exportable
    functions.
  - CompareToBackground: to correct the skewedness of o/e values towards
    long distances, computation of z.scores is now calculated using
    residuals from a polynomial model that fits the background couples
    (log(counts)~distance).
  - SearchPairs: added option to remove self interacting bins.
  - all internal functions are now in utilities.R.
  - Docs were reviewed.

                       Changes in version 0.99.2                        

  - Implemented import of corrected matrices for data in .hic and
    cool/mcool format.
  - Implemented import of O/E matrix for data in .hic format.
  - Implemented import of raw data in .h5 format.
  - Added GetInfo function to get info on a hic data (.hic,
    cool/mcool/h5 formats).
  - Removed dependency to BSDA::z.test in CompareToBackground.
  - Removed dependency to InteractionSet and added it as package to
    import in NAMESPACE to remove the PackageStartUpMessages.
  - Removed chatty package start up message and replaced it with nicer
    message.
  - Some BiocCheck NOTES were also takedn into consideration: changing
    sapply to vapply etc.

                       Changes in version 0.99.1                        

  - Corrected with Bioconductor's reviews
  - Added PrepareMtxList, ImportLoops, plotMultiAPA &
    CompareToBackground functions
  - Corrected bugs on seqlevels consistancy and name column for GRanges
    objects
  - Encapsulated small and internal functions in utilities.R
  - ExtractSubMatrix has option to remove duplicated submatrices
  - Corrected quantilization operations in Aggregation
  - Corrected over all code with suggestions from BiocCheck

                       Changes in version 0.99.0                        

  - Submitted to Bioconductor