NEWS.md
In dzhang32/dasper: Detecting abberant splicing events from RNA-sequencing data

dasper 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.

dasper 1.3.8

NEW FEATURES

Fix bug related to pkgdown::deploy_to_branch().

dasper 1.3.6

NEW FEATURES

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

dasper 1.3.2

NEW FEATURES

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

dasper 1.1.1

NEW FEATURES

Use of testthat edition 3 and parrallel running of tests.

dasper 0.99.2

NEW FEATURES

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

dasper 0.99.1

NEW FEATURES

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

dasper 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.