Changes in version 0.99.9                        

  - FIXED: igvShiny code now correctly handles the new internal GRanges
    binding profile data objects

                       Changes in version 0.99.8                        

  - Unicode removed from documentation to allow latex generation :/

                       Changes in version 0.99.6                        

  - NEW: Differential analyses now optionally screen out loci with
    negative signal in a specified number of replicates per sample
    (default is 2). These loci are removed before differential analysis.
  - NEW: Geneset universe calculations now take into account the
    low-signal screening; universe is determined only on the loci
    passing filter.
  - NEW: Loci labels are optionally sampled to allow labels even in
    highly-dense plot regions. Sampling algorithm determines a KNN graph
    from points, then uses this to select only a subset of total
    labelled points. A default parameter is provided, but all algorithm
    parameters are fully customisable.
  - NEW: Test conditions specified via the cond parameter can now use
    regexes, when regex = TRUE is set.
  - CHANGED: Test conditions specified via cond now use a simple named
    vector, merging cond and cond_names.
  - CHANGED: Improved and fixed underlying logic and tests to handle the
    cond parameter change
  - CHANGED: Substantially improved legend guide handling parameters and
    logic for volcano plots
  - FIXED: a number of minor bugfixes, code refactoring and tidying.

                       Changes in version 0.99.4                        

  - NEW: Added in FDR modelling and calculation routines for RNA
    Polymerase occupancy
  - NEW: plot_volcano and plot_venn functions can now filter for FDR
    when plotting
  - NEW: expressed() accessor method for obtaining all genes passing an
    FDR threshold for a specific condition
  - CHANGED: binding profile data is now stored as a GRanges object
  - CHANGED: analyse_go_terms now returns the clusterProfiler results
    object for downstream use
  - Begun incorporating gseGO functionality into analyse_go_terms
  - Improved documentation of DamIDResults class and accessors
  - Added more details to the package vignette
  - Many small bug fixes

                       Changes in version 0.99.2                        

  - NEW: Added button in IGV viewer to save SVG (useful when viewing
    window is horizontally compressed and button in the IGV interface is
    not displayed)
  - NEW: New legend customisation options for volcano plots (including a
    legend internal to the plot frame, now default)
  - NEW: More GO term plot customisation options
  - FIXED: All volcano plot point labels are now rendered as a single
    geom layer, preventing ugly overlaps
  - Substantial internal refactoring
  - Many small bug fixes
  - Updated unit tests

                       Changes in version 0.99.0                        

  - Initial submission to Bioconductor.