Package: SpaceTrooper 1.3.3

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:Dario Righelli [aut, cre], Benedetta Banzi [aut], Matteo Marchionni [aut], Oriana Romano [ctb], Mattia Forcato [ctb], Silvio Bicciato [aut], Davide Risso [ctb]

SpaceTrooper_1.3.3.tar.gz
SpaceTrooper_1.3.3.zip(r-4.7-any)SpaceTrooper_1.3.3.zip(r-4.6-any)SpaceTrooper_1.3.3.zip(r-4.5-any)
SpaceTrooper_1.3.3.tgz(r-4.6-any)SpaceTrooper_1.3.3.tgz(r-4.5-any)
SpaceTrooper_1.3.3.tar.gz(r-4.7-any)SpaceTrooper_1.3.3.tar.gz(r-4.6-any)
SpaceTrooper_1.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpaceTrooper/json (API)

# Install 'SpaceTrooper' in R:

install.packages('SpaceTrooper', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/drighelli/spacetrooper/issues

On BioConductor:SpaceTrooper-1.3.3(bioc 3.24)SpaceTrooper-1.2.0(bioc 3.23)

software transcriptomics geneexpression qualitycontrol spatial singlecell dataimport immunooncology

8.40 score 13 stars 1 packages 50 scripts 386 downloads 45 exports 178 dependencies

Last updated from:95265069ca. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	281
linux-devel	OK	509
source / vignettes	OK	361
linux-release	OK	499
macos-release	OK	378
macos-oldrel	OK	330
windows-devel	OK	376
windows-release	OK	380
windows-oldrel	OK	378
wasm-release	OK	206

Exports:.getActiveGeometryName .renameGeometry .setActiveGeometry addPolygonsToSPE applyQCScoreModel applyQScoreModel checkOutliers computeAreaFromPolygons computeAspectRatioFromPolygons computeCenterFromPolygons computeLambda computeMissingMetricsMerfish computeMissingMetricsXenium computeOutliersQCScore computeOutliersQScore computeQCScore computeQCScoreFlags computeQScore computeQScoreFlags computeSpatialOutlier computeThresholdFlags computeTrainDF getFencesOutlier getModelFormula plotCellsFovs plotCentroids plotMetricHist plotPolygons plotQScoreTerms plotZoomFovsMap qcFlagPlots readAndAddPolygonsToSPE readCosmxProteinSPE readCosmxSPE readMerfishSPE readPolygons readPolygonsCosmx readPolygonsMerfish readPolygonsXenium readXeniumSPE spatialPerCellQC trainModel updateCosmxProteinSPE updateCosmxSPE updateXeniumSPE

Dependencies:abind arrow askpass assertthat assorthead backports beachmat beeswarm BH Biobase BiocFileCache BiocGenerics biocmake BiocNeighbors BiocParallel BiocSingular bit bit64 blob boot broom cachem car carData class classInt cli codetools colorspace corrplot cowplot cpp11 curl data.table DBI dbplyr DelayedArray DelayedMatrixStats DEoptimR Deriv dir.expiry doBy dplyr dqrng DropletUtils e1071 edgeR farver fastmap filelock FNN foreach forecast formatR Formula fracdiff futile.logger futile.options generics GenomicRanges geometries ggbeeswarm ggplot2 ggpubr ggrepel ggsci ggsignif glmnet glue gridExtra gtable h5mread HDF5Array httr2 IRanges irlba isoband iterators KernSmooth labeling lambda.r lattice lifecycle limma lme4 lmtest locfit magick magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv minqa modelr nlme nloptr nnet numDeriv openssl pbkrtest pheatmap pillar pkgconfig polynom proxy purrr quantreg R.methodsS3 R.oo R.utils R6 rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress Rdpack reformulas rhdf5 rhdf5filters Rhdf5lib rjson rlang robustbase RSpectra RSQLite rstatix rsvd Rtsne s2 S4Arrays S4Vectors S7 ScaledMatrix scales scater scuttle Seqinfo sf sfheaders shape SingleCellExperiment sitmo snow SparseArray SparseM sparseMatrixStats SpatialExperiment SpatialExperimentIO statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate units urca utf8 uwot vctrs vipor viridis viridisLite withr wk XVector zoo

CosMx Protein Assay Data Quality Control with SpaceTrooper

Rendered fromProtein_tutorial_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-10-09
Started: 2026-01-26

Imaging-based Spatial Transcriptomics Data Quality Control with SpaceTrooper

Rendered fromRNA_tutorial_vignette.rmdusingknitr::rmarkdown

Last update: 2026-10-09
Started: 2026-01-26

SpaceTrooper utilities overview

Rendered fromSpaceTrooper_utilities.Rmdusingknitr::rmarkdown

Last update: 2026-10-09
Started: 2026-02-09

Loading CosMx and Xenium data with SpaceTrooper

Rendered frominteroperability.Rmdusingknitr::rmarkdown

Last update: 2026-01-26
Started: 2026-01-26

Help page	Topics
.getActiveGeometryName	.getActiveGeometryName
.renameGeometry	.renameGeometry
.setActiveGeometry	.setActiveGeometry
addPolygonsToSPE	addPolygonsToSPE
applyQScoreModel	applyQScoreModel
checkOutliers	checkOutliers
computeAreaFromPolygons	computeAreaFromPolygons
computeAspectRatioFromPolygons	computeAspectRatioFromPolygons
computeCenterFromPolygons	computeCenterFromPolygons
computeLambda	computeLambda
computeMissingMetricsMerfish	computeMissingMetricsMerfish
computeMissingMetricsXenium	computeMissingMetricsXenium
computeOutliersQScore	computeOutliersQScore
computeQScore	computeQScore
computeQScoreFlags	computeQScoreFlags
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
Deprecated functions in SpaceTrooper	applyQCScoreModel computeOutliersQCScore computeQCScore computeQCScoreFlags SpaceTrooper-deprecated
spatialPerCellQC	spatialPerCellQC
trainModel	trainModel
updateCosmxProteinSPE	updateCosmxProteinSPE
updateCosmxSPE	updateCosmxSPE
updateXeniumSPE	updateXeniumSPE

Package: SpaceTrooper 1.3.3

SpaceTrooper: SpaceTrooper performs Quality Control analysis of Image-Based spatial

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