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