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NEWS.md

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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.