Changes in version 0.8                         

  - removed deprecated functions
  - removed old function names

                        Changes in version 0.7.1                        

  - new Bioconductor style names for functions alongside original
    function names
  - updated gene ontology plot

                        Changes in version 0.7.0                        

New features

  - updated gene ontology output of results
  - gene ontology plot fn plot_gene_ontology()
  - all functions operate case-insensitive - allow for .bam or .BAM and
    same with dam or Dam
  - replaced "Downreg" meth_status with "No_sig"
  - new peak function available
  - updates to plot functions - fixed wrap plot, set colours for count
    plot
  - added new gene fn that uses a TxDb object or biomaRt
    (get_genes_biomaRt has been deprecated and will be removed)
  - example count data available through data(dros_counts)

                        Changes in version 0.6.0                        

Removed features

  - removed process_bams_old as dependency exomeCopy has been
    deprecated.

                        Changes in version 0.5.0                        

Removed features

  - regions_gatc_drosophila_dm6 is no longer available as a data file
    upon loading. Can be made with gatc_region_fn()

                        Changes in version 0.4.0                        

New features

  - process_bams() new count method using Rsubread::featureCounts()
    allowing for fractional counts and differentiating between single
    and paired end BAM files
  - edgeR_set_up() filter out large regions (> 10kb)
  - aggregate_peaks() new method for ranking peaks based on theory of
    csaw::getBestTest()
  - aggregate_peaks() retain small peaks so that they are able to be
    combined with the gaps fn
  - gatc_track() simplified for one argument input - identifies if input
    is BSgenome or FASTA

Bug fixes

  - geom_genes can now handle a region of only introns - previously
    threw an error

                        Changes in version 0.3.1                        

New features

  - Plotting options - counts layout and log2 scale, and peak_id text
  - New default for differential testing: p-value set to 0.01

                        Changes in version 0.3.0                        

Bug fixes

  - streamlined outputs
  - removed obselete functions

                        Changes in version 0.2.0                        

New features

  - New peak output and functionality (combines peaks with small gaps)
  - New genes output - with list of 3 data.frames
  - Gene ontology fn
  - Plot_wrap() - plot all at once
  - gatc_track() - create the GATC track

Bug fixes

  - accurate plotting

Documentation

  - runnable examples

                        Changes in version 0.1.0                        

  - Added a NEWS.md file to track changes to the package.
  - Added geom_genes.me allowing for genes plot
  - Fixed geom_peak.new