NEWS

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SpaceTrooper 1.3.3

• minor changes in vignettes to get lighter images

SpaceTrooper 1.3.2

• Updaging vignette with details on xenium_small dataset

SpaceTrooper 1.3.1

• Added the canonical computeQScore(), computeQScoreFlags(), computeOutliersQScore(), and applyQScoreModel() APIs.
• Retained computeQCScore(), computeQCScoreFlags(), computeOutliersQCScore(), and applyQCScoreModel() as deprecated compatibility APIs. They preserve historical arguments, QC_score, low_qcscore, low_threshold_qcscore, and QCScore_model* metadata.
• Restored historical plotting arguments (size, alpha, alphaNumbers, csize, calpha, mapNumbersCol, and mapAlphaNumbers) as aliases for the canonical plotting arguments. Canonical arguments take precedence when both forms are supplied.
• Restored getModelFormula(formulaVars, verbose=FALSE) compatibility while accepting metricList as a named replacement.
• Restored the public computeLambda(trainDF, modelFormula) signature, complete-case filtering, and support for both qcscore_train and QScore_train.
• User-supplied modelFormula values are now fitted without adding, removing, or rebuilding terms. Supported subsets, additive formulas, and selected interactions are preserved.
• Supported base QC metrics selected by a custom modelFormula now determine the outliers, good and bad cells, and QScore_train used for model training; omitted metrics no longer contribute to training-label construction.
• Formula predictors are limited to log2SignalDensity, Area_um, log2AspectRatio, and log2Ctrl_total_ratio. Unsupported predictors and transformations now produce informative errors, and CosMx-only border terms are checked against dataset technology.
• Model transfer now has a canonical public API, preserves training matrix column order, supports validated custom formulas, and retains the historical deprecated interface.
• Fixed the SpaceTrooper utilities vignette name and added the bioRxiv citation.
• Follow-up: intercept handling remains unchanged in this release and should be reviewed consistently across training, lambda selection, prediction, and model transfer.

SpaceTrooper 1.1.7

• fixing author name typo

SpaceTrooper 1.1.6

• adding new vignette about SpaceTrooper utilities

SpaceTrooper 1.1.5

• minor enhancement of cosmx input reading, polygonsCol added
• minor documentation clarification on QCScore computation
• cleaned LICENSE stub and creating LICENSE.md file

SpaceTrooper 1.1.4

• updating documentation along multiple functions
• adding graphical abstract
• updating README
• updating Vignettes and providing better data examples

SpaceTrooper 1.1.3

• fixing verbose message in QC functions.

SpaceTrooper 1.1.2

• adding volume instead of area for MERFISH.
• refactoring log2CountArea to log2DensitySignal
• added size and alpha arguments to plotCellsFovs
• added scaleBar argument to plotCellsFovs, plotCentroids, plotPolygons and plotZoomFovsMap

SpaceTrooper 1.0.1

• fixing minor bugs in AspectRatio internal computation for technology missing it.
• fixing merfish reading where colData where not properly sorted and sync with assay cells.

SpaceTrooper 0.99.0

• adding unit tests on QC steps
• adding datasets descriptions