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1. Commits on Oct 12, 2026

   • refactor: route conversion verbosity through thisutils helpers (#493)

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   • wip(scenicplus): native SCENIC+ backend in C++ with tests (#492)

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2. Commits on Oct 11, 2026

   • fix: preserve clustering results across subset and rename (#486)

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3. Commits on Oct 10, 2026

   • docs: clarify six full-input workflows and article navigation (#488)

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4. Commits on Oct 9, 2026

   • Merge pull request #485 from hurry060215-tech/fix/deconvolution-input-alignment-current-main-20261008

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   • Merge pull request #487 from hurry060215-tech/refactor/ccc-heatmap-post483

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   • test: align optional backend metadata with unpinned thisutils remote

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5. Commits on Oct 8, 2026

   • refactor: split CCCHeatmap data and layout helpers

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   • test: match the default thisutils remote metadata

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   • fix: align deconvolution inputs on current main

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   • fix: clean unused helpers and share duplicated internals (#483)

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   • fix: use the default thisutils remote (#484)

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6. Commits on Oct 7, 2026

   • fix: drop contribution guide and check_r example gates (#480)

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   • feat: improve BANKSY spatial analysis usability (#468)

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   • docs: clarify optional backend checks and exclude contribution guide from builds (#478)

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   • fix: handle missing optional GSVA in native scoring probes (#479)

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   • fix: align deprecated srt alias presence handling (#472)

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   • Refactor CCC internals and split cccplot.R (#471)

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   • Audit Suggests usage and exported help topics (#470)

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   • fix: standardize business condition logging (#473)

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   • refactor: split integration backend implementations (#475)

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   • refactor: narrow Seurat and ggplot2 imports (#476)

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   • docs: clarify logging and backend conventions (#469)

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   • fix: normalize species names before annotation database lookup (#477)

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   • fix: honor enrichment annotation and legend border settings (#467)

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   • feat: default label_insitu to TRUE in dim plots (#474)

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7. Commits on Oct 6, 2026

   • fix: defer scatterpie dependency checks for empty pie plots (#466)

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   • fix(RunSpatialNetwork): guard independent sample coordinate fields (#465)

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   • fix(RunBANKSY): guard independent sample coordinate fields (#464)

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   • fix(RunBayesSpace): honor selected metadata coordinates (#463)

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   • fix(RunCSIDE): align finite covariates with retained spot IDs (#462)

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   • fix(RunCytoSPACE): preserve cell identity and summary labels (#461)

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   • fix(RunMistyR): validate targets and independent spatial inputs (#460)

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   • fix(prep_ref): align reference metadata with selected assay cells (#459)

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   • Fix SpatialNeighborhoodPlot FDR colors and sample selection (#458)

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