Changes in version 1.3.2                        

New Features

  - Added the 'flagVisiumOutliers()' function to identify and flag
    systematic outlier spots in Visium datasets. This feature enhances
    data quality by allowing users to efficiently detect and exclude
    problematic spots from downstream analyses.

                        Changes in version 1.3.1                        

Major Changes

  - Function Renaming: The function plotQC has been renamed to
    plotQCmetrics to better reflect its purpose. The new function
    plotQCmetrics should be used moving forward. This change improves
    clarity in the package’s API by specifying that this function is
    designed for plotting QC metrics.

New Features and Enhancements

  - shape argument: Added a shape argument to findArtifacts, allowing
    users to specify the neighborhood shape as either "hexagonal" or
    "square" for local variance calculations. This enhancement provides
    flexibility for different spatial arrangements in spatial
    transcriptomics data.

  - Updated n_order parameter: Renamed the n_rings parameter to n_order
    in the findArtifacts function to better describe its purpose of
    specifying the N-order neighbors for local mitochondrial variance
    calculations.

  - Parallelization: Added a workers argument for parallel processing
    using BiocParallel in both localOutlier and localVariance functions.
    This allows for faster computation, particularly on larger datasets.

Deprecations

  - plotQC Function Deprecated: The plotQC function is now deprecated.
    While it remains available for backward compatibility, users are
    encouraged to transition to plotQCmetrics. Calling plotQC will
    display a warning, reminding users of the deprecation.

This change is backward compatible; existing code using plotQC will
still work but will show a warning. We recommend updating your code to
use plotQCmetrics to avoid any issues in future versions where plotQC
may be removed.