Changes in version 1.5.1                        

NEW FEATURES

  - Fix bug related to coverage_norm(), ensuring that regions used to
    normalise coverage have the same seqlevels as the inputted
    junctions.

                        Changes in version 1.3.8                        

NEW FEATURES

  - Fix bug related to pkgdown::deploy_to_branch().

                        Changes in version 1.3.6                        

NEW FEATURES

  - Add functionality to annotate junctions with gene_name/symbol using
    EnsDb inputted into junction_annot().

                        Changes in version 1.3.2                        

NEW FEATURES

  - Fix bugs within plot_sashimi() and enable the visualization of raw
    junction counts.

                        Changes in version 1.1.1                        

NEW FEATURES

  - Use of testthat edition 3 and parrallel running of tests.

                       Changes in version 0.99.2                        

NEW FEATURES

  - Merge documentation into one man page for junction, coverage and
    outlier processing functions to reduce runtime of roxygen examples.

                       Changes in version 0.99.1                        

NEW FEATURES

  - Change outlier_detect() to using basilisk for interfacing into
    python replacing reticulate.

                       Changes in version 0.99.0                        

NEW FEATURES

  - Converted dasper into a Bioconductor-friendly format using biocthis.
  - Added junction_load(), which loads raw junction data from
    RNA-sequencing into an RangedSummarizedExperiment object. Includes
    an option to allow download of user-specified control junctions.
  - Added junction_annot(), which uses information from reference
    annotation and the strand of a junction to classify junctions as
    "annotated", "novel_acceptor", "novel_donor", "novel_exon_skip",
    "novel_combo", "ambig_gene" and "unannotated".
  - Added junction_filter(), which filters junctions by their count,
    width, annotation or if they overlap a set of user-defined regions.
  - Added junction_norm(), which normalises raw junction counts (into a
    proportion-spliced-in) by dividing the counts of each junction by
    the total number of counts in it's associated cluster.
  - Added junction_process(), a wrapper function for all "junction_"
    prefixed functions except junction_load().
  - Added junction_score(), which scores patient junctions based on the
    extent their counts deviate from a control count distribution.
  - Added coverage_norm(), which will load and normalise coverage for
    exonic/intronic regions corresponding to each junction.
  - Added coverage_score(), which scores coverage associated with each
    junction based on it's deviation from control coverage
    distributions.
  - Added coverage_process(), a wrapper function for all "coverage_"
    prefixed functions.
  - Added outlier_detect(), which uses the junction scores and coverage
    scores as input into an unsupervised outlier detection algorithm to
    find the most outlier-looking junctions in each sample.
  - Added outlier_aggregate(), which aggregates the junction-level
    outlier data to a cluster-level.
  - Added outlier_process(), a wrapper function for all "outlier_"
    prefixed functions.
  - Added plot_sashimi(), which enables the visualisation of junction
    data across genes/transcripts or regions of interest.