scPairs

• **Rationalised examples**: nine exported functions now run plain R examples during R CMD check. Two functions (AssessGenePair, PlotPairSummary) are wrapped in \donttest{} because their examples exceed the five-second threshold on the check servers. Three functions retain \dontrun{} because they require software not guaranteed to be present: PlotPairSpatial (spatial-assay Seurat object), PlotBridgeNetwork and PlotPairSynergy (Bioconductor annotation packages org.Hs.eg.db / org.Mm.eg.db).
• **Removed set.seed()** from inside .plot_bridge_network_enhanced() (R/plot_synergy.R); the package no longer modifies the user's RNG state.
• **Fixed Unicode in documentation**: replaced non-ASCII characters (U+2248 approximately-equal, U+00D7 multiplication sign, U+2013/U+2014 dashes) in scpairs_testdata Rd documentation with ASCII equivalents, resolving the LaTeX PDF-manual build error.
• **Fixed invalid URI in README.md**: the LICENSE.md hyperlink now points to the full GitHub URL rather than a bare file path, removing the URI validity note.
• **Added inst/WORDLIST** listing domain-specific terms (Jaccard, KEGG, KNN, midcorrelation, transcriptomics, etc.) to suppress false-positive spell-check notes.

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Built-in Test Dataset

• **New dataset scpairs_testdata** (data/scpairs_testdata.rda, 26 KB): a synthetic Seurat object (100 cells, 20 genes, 3 balanced clusters, 5-component PCA, 2-D UMAP) with two injected co-expression patterns:
• **GENE3 & GENE4**: globally correlated across all cells (Pearson r approximately 0.89 in normalised data).
• **GENE1 & GENE2**: moderately correlated within cluster 1 only.
• All remaining pairs: near-independent noise.
• Generation script provided in data-raw/make_testdata.R (set.seed(7391)); data-raw/ is excluded from the CRAN build via .Rbuildignore.
• All runnable examples reference scpairs_testdata directly, eliminating the need for inline Seurat-object construction in any function documentation.
• Dataset documented in R/scpairs_testdata.R with @format, @details, @usage, @source, @seealso, and @family Section_0_Data tags.

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Documentation Improvements

• **Completed documentation** for PlotPairSummary() (added @examples, improved @return) and PlotPairSynergy() (added @examples with \dontrun{}, expanded @return for all four panels).
• **Added @family tags** grouping all exported functions into three help families:
• Section_0_Data -- scpairs_testdata
• Section_1_Discovery -- FindAllPairs, FindGenePairs, AssessGenePair
• Section_2_Visualization -- all eleven PlotPair* and PlotBridgeNetwork functions
• **Added @seealso cross-references** throughout, linking each function to its most closely related counterparts.
• **Improved @return descriptions** for PlotPairDimplot, PlotPairViolin, PlotPairScatter, PlotPairSmoothed, PlotPairSummary, PlotPairCrossType, PlotPairSpatial, PlotPairNetwork, and PlotPairHeatmap.

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Package Structure

• R/data.R renamed to R/scpairs_testdata.R, following the convention of naming dataset documentation files after the dataset itself.
• tests/README.md added: documents test categories, expected behaviour, coverage targets, and a contribution template.
• Six demonstration plots saved to docs/ from scpairs_testdata: scpairs_network.png, scpairs_heatmap.png, scpairs_dimplot.png, scpairs_smoothed.png, scpairs_violin.png, scpairs_scatter.png.
• README.md restructured: CRAN/GitHub badges, right-aligned logo, full table of contents, collapsible dependency section, Visualization Gallery embedding the six demo images, and an expanded Functions reference table.

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Test Suite

• All seven test files updated to use scpairs_testdata directly, removing per-test Seurat pipeline construction and improving reproducibility. create_test_seurat() is retained in helper-test_data.R for edge-case tests requiring custom configurations (single-cluster data, spatial coordinates, unusual gene counts).
• **Two latent test warnings resolved**:
• test-assess-pair.R: the n_perm = 49 call is now wrapped in suppressWarnings() -- the low-permutation advisory is intentional package behaviour, not a test defect.
• test-consolidated-functions.R: the third matrix row in the .compute_ratio_consistency batch test now uses abs(rnorm(n)) to prevent log2(mat + 1) from receiving negative inputs.
• **115 tests passing**, 0 failures, 0 warnings, 0 skips.

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