Skip to contents

Changelog

Source: NEWS.md

Matisse 0.1.0

Initial release

  • New MatisseObject S4 class wrapping a Seurat object with isoform-resolved layers: junction counts, PSI matrix, inclusion/exclusion counts, event and junction annotation tables, and per-cell isoform metadata.
  • CreateMatisseObject(): primary constructor with input validation and automatic cell-barcode alignment.
  • CalculatePSI(): computes PSI matrices from junction count data and splice event definitions. Supports both MatisseObject and bare matrix input.
  • SummarizePSI(): per-event summary statistics (mean, median, sd, coverage).
  • ComputeIsoformQC(): per-cell QC metrics including junction detection rate, total junction reads, event coverage, and mean PSI.
  • FilterCells() and FilterEvents(): threshold-based filtering with informative removal summaries.
  • Visualization: PlotPSIUMAP(), PlotPSIViolin(), PlotPSIHeatmap(), PlotJunctionCoverage(), PlotQCMetrics().
  • BuildSimpleEvents(): convenience helper for generating one-vs-rest event tables from a junction annotation.
  • MergeMatisse(): concatenate two MatisseObjects with cell-prefix deduplication.
  • GitHub Actions workflows for R CMD check (multi-OS), pkgdown website deployment, and test coverage reporting.