v0.2.2

Fixed
RANSAC sampled the wrong events. The random sample was drawn against the quadrant-subset size but used to index the full dataset, so initial models were fit on arbitrary rows instead of the upper-right-quadrant events the algorithm targets. Sampling now uses the actual quadrant row indices.
Quadrant cutoff was miscomputed. The 50% threshold used half the data range ((max − min) / 2), which is only correct when the minimum is 0; wrong for the offset/negative values typical of asinh/biexponential-transformed data. It’s now the midpoint of the 1st–99th-percentile range, which is also robust to a few very bright events that previously skewed the cutoff.
Inlier sets are now combined with union() so the seed sample and residual-based inliers are consistently indexed.

Added
Input validation on formula, data, and numeric parameters.
Graceful skip (returns NULL with a warning) when too few events fall in the quadrant, instead of erroring inside sample().

Impact: aggregate calls from 0.2.1 and earlier should be re-run; results will differ (and improve), especially on transformed data and channels with bright outliers.

v0.2.1

Add unit tests and input validation for key algorithmic functions

• Add tests for compensate_data(), DE_pseudobulk(), run_FlowSOM(),
  run_modified_ransac(), and detect_aggregates(), which previously
  had no coverage.
• Add input validation with informative error messages to the same
  functions (class checks, missing/invalid args, mismatched columns).
• Fix a 1:nrow() indexing bug in detect_aggregates() that misbehaved
  on a zero-row aggregate_channels data frame.

v0.2.0

Breaking changes

• Seurat >= 5.0.0 is now required.
• Migrated from the deprecated slot argument to layer throughout, for compatibility with SeuratObject >= 5.0.0.

Features

• Added optional TMM normalization to differential_abundance() (tmm_normalisation, default FALSE) to correct for compositional effects.

Improvements

• Aggregate detection functions now skip unfittable channel pairs with an informative warning instead of failing.
• Added a testthat unit test suite.

Documentation

• Updated vignette text and added a cyCombine usage example.

v0.1.1

New features implemented:

• FlowSOM clustering
• Conversion of Seurat Objects to flowFrame, flowSet and SingleCellExperiment
• Bead normalisation for Mass cytometry data

Changes to existing functions:

• Derandomization feature for create_seurat function
• Updated export_fcs function (can now export all types of Seurat assays)
• Updated vignette.

Initial Release (v0.1.0)

Initial Release