Changes in version 2.3.1                        

New SpaceMarkersExperiment class

  - Added SpaceMarkersExperiment (SME), an S4 class extending
    SpatialExperiment that carries hotspots, influence maps, and pattern
    metadata alongside expression and spatial coordinates.
  - Added SME-aware methods and dispatch for get_spatial_features,
    get_interacting_genes, get_pairwise_interacting_genes, and related
    accessors so users can stay in a single Bioconductor object
    end-to-end.
  - Re-exported SpatialExperiment / SummarizedExperiment accessors so
    SME workflows do not require attaching upstream packages.

AnnData I/O

  - Added load_anndata() to read .h5ad files directly into a
    SpaceMarkersExperiment.
  - Added save_anndata() to write SME objects back to .h5ad with
    round-trip fidelity.
  - Added direct SingleCellExperiment → SpaceMarkersExperiment coercion.

Directed interaction analysis and visualization

  - Added overlap_map() for per-spot directed interaction classification
    (3-level factor per direction).
  - plot_spatial() gained a source argument
    (colData/assay/hotspots/influence_map/interaction) and directed
    interaction labels for three-way hotspot overlays.
  - Hotspot plots in vignettes now use distinct colors per pattern.

Vignettes

  - New SpaceMarkersExperiment_vignette walks through the SME-first
    workflow.
  - SpaceMarkersStepByStep_vignette restructured as a tutorial with
    per-step plots interleaved with narrative.
  - Vignette data downloads now route through BiocFileCache instead of
    ad hoc temp files.
  - Compact JPEG raster output keeps rendered HTML vignettes under
    Bioconductor's per-file size guideline.

Bioconductor readiness

  - Runnable examples and \value sections added across exported
    functions for BiocCheck.
  - Tightened .Rbuildignore and .gitignore for a clean source tarball.
  - Renamed R/OneSpaceMarkers.R → R/SpaceMarkers.R and regenerated
    Collate order.

Performance

  - Avoided dense coercion in the gene filter and skipped materializing
    the spPatterns data frame, reducing memory pressure on large
    samples.

                        Changes in version 2.0.0                        

  - Added support for directed cell-cell interaction (see
    calculate_gene_scores_directed, calculate_influence)
  - Functions for supporting ligand-receptor interactions based on
    directed cell-cell interactions
  - Added ligand–receptor and gene-set scoring utilities:
    calculate_lr_scores, calculate_gene_set_score, and
    calculate_gene_set_specificity.
  - Added support for handling Visium HD
  - plotting functions using circlize for showing ligand-receiver
    interactions.
  - API and naming standardization (backwards-incompatible) Major public
    functions renamed to snake_case for consistency (examples:
    calcInfluence → calculate_influence, getInteractingGenes →
    get_interacting_genes, getPairwiseInteractingGenes →
    get_pairwise_interacting_genes, getSpatialFeatures →
    get_spatial_features, getSpatialParameters → get_spatial_parameters)

                        Changes in version 1.5.0                        

  - Added findAllHotspots to use with getPairwiseInteractingGenes
  - Return empty interacting genes list instead of failing with error
    when no genes pass fdr threshold.

                        Changes in version 1.2.0                        

  - Updated SpaceMarkersMetric by fixing signage and log transformed to
    scale magnitude
  - Added get_spatial_paramsExternal which enables getting spatial
    parameters from file or from the user.
  - Deprecated getSpatialParameters
  - Enabled includeSelf = TRUE in getInteractingGenes.R to improve
    hotspot detection
  - Enabled load10XCoords to read coordinates from VisiumHD directory
  - Optimized the long running row.dunn.test() function
  - Corrected sparse -> dense conversions
  - Added getPairwiseInteractingGenes which enables pairwise analysis of
    interacting patterns
  - getSpatialFeatures: add default method to infer the object passed to
    it.

                        Changes in version 0.1.0                        

  - Added a NEWS.md file to track changes to the package.