Package: SpaceTrooper 1.2.0
Dario Righelli
SpaceTrooper: SpaceTrooper performs Quality Control analysis of Image-Based spatial
SpaceTrooper performs Quality Control analysis using data driven GLM models of Image-Based spatial data, providing exploration plots, QC metrics computation, outlier detection. It implements a GLM strategy for the detection of low quality cells in imaging-based spatial data (Transcriptomics and Proteomics). It additionally implements several plots for the visualization of imaging based polygons through the ggplot2 package.
Authors:
SpaceTrooper_1.2.0.tar.gz
SpaceTrooper_1.2.0.zip(r-4.7)SpaceTrooper_1.2.0.zip(r-4.6)SpaceTrooper_1.2.0.zip(r-4.5)
SpaceTrooper_1.2.0.tgz(r-4.6-any)SpaceTrooper_1.2.0.tgz(r-4.5-any)
SpaceTrooper_1.2.0.tar.gz(r-4.7-any)SpaceTrooper_1.2.0.tar.gz(r-4.6-any)
SpaceTrooper_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SpaceTrooper/json (API)
NEWS
| # Install 'SpaceTrooper' in R: |
| install.packages('SpaceTrooper', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/drighelli/spacetrooper/issues
On BioConductor:SpaceTrooper-1.3.0(bioc 3.24)SpaceTrooper-1.2.0(bioc 3.23)
softwaretranscriptomicsgeneexpressionqualitycontrolspatialsinglecelldataimportimmunooncology
Last updated from:ab9860591a (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 370 | ||
| linux-devel-x86_64 | OK | 441 | ||
| source / vignettes | OK | 351 | ||
| linux-release-x86_64 | OK | 453 | ||
| macos-release-arm64 | OK | 267 | ||
| macos-oldrel-arm64 | OK | 250 | ||
| windows-devel | OK | 367 | ||
| windows-release | OK | 396 | ||
| windows-oldrel | OK | 406 | ||
| wasm-release | OK | 208 |
Exports:.getActiveGeometryName.renameGeometry.setActiveGeometryaddPolygonsToSPEcheckOutlierscomputeAreaFromPolygonscomputeAspectRatioFromPolygonscomputeCenterFromPolygonscomputeLambdacomputeMissingMetricsMerfishcomputeMissingMetricsXeniumcomputeOutliersQCScorecomputeQCScorecomputeQCScoreFlagscomputeSpatialOutliercomputeThresholdFlagscomputeTrainDFgetFencesOutliergetModelFormulaplotCellsFovsplotCentroidsplotMetricHistplotPolygonsplotQScoreTermsplotZoomFovsMapqcFlagPlotsreadAndAddPolygonsToSPEreadCosmxProteinSPEreadCosmxSPEreadMerfishSPEreadPolygonsreadPolygonsCosmxreadPolygonsMerfishreadPolygonsXeniumreadXeniumSPEspatialPerCellQCtrainModelupdateCosmxProteinSPEupdateCosmxSPEupdateXeniumSPE
Dependencies:abindarrowaskpassassertthatassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocNeighborsBiocParallelBiocSingularbitbit64blobbootbroomcachemCairocarcarDataclassclassIntclicodetoolscolorspacecorrplotcowplotcpp11curldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDEoptimRDerivdir.expirydoBydplyrdqrngDropletUtilse1071edgeRfarverfastmapfilelockFNNforeachforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesgeometriesggbeeswarmggplot2ggpubrggrastrggrepelggsciggsignifglmnetgluegridExtragtableh5mreadHDF5Arrayhttr2IRangesirlbaisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalme4lmtestlocfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkminqamodelrnlmenloptrnnetnumDerivopensslpbkrtestpheatmappillarpkgconfigpngpolynomproxypurrrquantregR.methodsS3R.ooR.utilsR6raggrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRdpackreformulasrhdf5rhdf5filtersRhdf5librjsonrlangrobustbaseRSpectraRSQLiterstatixrsvdRtsnes2S4ArraysS4VectorsS7ScaledMatrixscalesscaterscuttleSeqinfosfsfheadersshapeSingleCellExperimentsitmosnowSparseArraySparseMsparseMatrixStatsSpatialExperimentSpatialExperimentIOstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttimeDateunitsurcautf8uwotvctrsviporviridisviridisLitewithrwkXVectorzoo
CosMx Protein Assay Data Quality Control with SpaceTrooper
Rendered fromProtein_tutorial_vignette.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-01-26
Started: 2026-01-26
Imaging-based Spatial Transcriptomics Data Quality Control with SpaceTrooper
Rendered fromRNA_tutorial_vignette.rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-01-26
Started: 2026-01-26
SpaceTrooper utilities overview
Rendered fromSpaceTrooper_utilities.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-02-09
Started: 2026-02-09
Loading CosMx and Xenium data with SpaceTrooper
Rendered frominteroperability.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-01-26
Started: 2026-01-26
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| .getActiveGeometryName | .getActiveGeometryName |
| .renameGeometry | .renameGeometry |
| .setActiveGeometry | .setActiveGeometry |
| addPolygonsToSPE | addPolygonsToSPE |
| checkOutliers | checkOutliers |
| computeAreaFromPolygons | computeAreaFromPolygons |
| computeAspectRatioFromPolygons | computeAspectRatioFromPolygons |
| computeCenterFromPolygons | computeCenterFromPolygons |
| computeLambda | computeLambda |
| computeMissingMetricsMerfish | computeMissingMetricsMerfish |
| computeMissingMetricsXenium | computeMissingMetricsXenium |
| computeOutliersQCScore | computeOutliersQCScore |
| computeQCScore | computeQCScore |
| computeQCScoreFlags | computeQCScoreFlags |
| computeSpatialOutlier | computeSpatialOutlier |
| computeThresholdFlags | computeThresholdFlags |
| computeTrainDF | computeTrainDF |
| getFencesOutlier | getFencesOutlier |
| getModelFormula | getModelFormula |
| plotCellsFovs | plotCellsFovs |
| plotCentroids | plotCentroids |
| plotMetricHist | plotMetricHist |
| plotPolygons | plotPolygons |
| plotQScoreTerms | plotQScoreTerms |
| plotZoomFovsMap | plotZoomFovsMap |
| qcFlagPlots | qcFlagPlots |
| readAndAddPolygonsToSPE | readAndAddPolygonsToSPE |
| readCosmxSPE | readCosmxProteinSPE readCosmxSPE |
| readMerfishSPE | readMerfishSPE |
| readPolygons | readPolygons |
| readPolygonsCosmx | readPolygonsCosmx |
| readPolygonsMerfish | readPolygonsMerfish |
| readPolygonsXenium | readPolygonsXenium |
| Load data from a 10x Genomics Xenium experiment | readXeniumSPE |
| spatialPerCellQC | spatialPerCellQC |
| trainModel | trainModel |
| updateCosmxProteinSPE | updateCosmxProteinSPE |
| updateCosmxSPE | updateCosmxSPE |
| updateXeniumSPE | updateXeniumSPE |
