Package: scDiagnostics 1.7.0

Anthony Christidis

scDiagnostics: Cell type annotation diagnostics

The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes.

Authors:Anthony Christidis [aut, cre], Andrew Ghazi [aut], Smriti Chawla [aut], Nitesh Turaga [ctb], Ludwig Geistlinger [aut], Robert Gentleman [aut]

scDiagnostics_1.7.0.tar.gz
scDiagnostics_1.7.0.zip(r-4.7)scDiagnostics_1.7.0.zip(r-4.6)scDiagnostics_1.7.0.zip(r-4.5)
scDiagnostics_1.7.0.tgz(r-4.6-any)scDiagnostics_1.7.0.tgz(r-4.5-any)
scDiagnostics_1.7.0.tar.gz(r-4.7-any)scDiagnostics_1.7.0.tar.gz(r-4.6-any)
scDiagnostics_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scDiagnostics/json (API)
NEWS

# Install 'scDiagnostics' in R:
install.packages('scDiagnostics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ccb-hms/scdiagnostics/issues

On BioConductor:scDiagnostics-1.7.0(bioc 3.24)scDiagnostics-1.6.0(bioc 3.23)

annotationclassificationclusteringgeneexpressionrnaseqsinglecellsoftwaretranscriptomics

8.05 score 13 stars 67 scripts 255 downloads 32 exports 81 dependencies

Last updated from:dadd633a84. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING314
linux-devel-x86_64WARNING748
source / vignettesOK497
linux-release-x86_64WARNING735
macos-release-arm64WARNING385
macos-oldrel-arm64WARNING531
windows-develWARNING2100
windows-releaseWARNING1709
windows-oldrelWARNING2129
wasm-releaseOK265

Exports:boxplotPCAcalculateAveragePairwiseCorrelationcalculateCategorizationEntropycalculateCellDistancescalculateCellDistancesSimilaritycalculateCellSimilarityPCAcalculateCramerPValuecalculateDiscriminantSpacecalculateGeneShiftscalculateGraphIntegrationcalculateHotellingPValuecalculateHVGOverlapcalculateMMDPValuecalculateSIRSpacecalculateVarImpOverlapcalculateWassersteinDistancecompareMarkerscomparePCAcomparePCASubspacedetectAnomalyhistQCvsAnnotationplotCellTypeMDSplotCellTypePCAplotGeneExpressionDimredplotGeneSetScoresplotMarkerExpressionplotPairwiseDistancesDensityplotQCvsAnnotationprocessPCAprojectPCAprojectSIRregressPC

Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelblusterbootcliclustercodetoolscpp11cramercrayondata.tableDelayedArraydplyrfarverFNNforcatsformatRfutile.loggerfutile.optionsgenericsGenomicRangesGGallyggplot2ggridgesggstatsgluegtablehmsigraphIRangesisobandisotreejsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatspatchworkpillarpkgconfigprettyunitsprogresspurrrR6rangerRColorBrewerRcppRcppEigenRhpcBLASctlrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttransportutf8vctrsviridisLitewithrXVector

Getting Started with scDiagnostics

Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga, Ludwig Geistlinger, Robert Gentleman

Rendered fromscDiagnostics.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-10-03
Started: 2023-08-04

Visualization of Cell Type Annotations

Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga, Ludwig Geistlinger, Robert Gentleman

Rendered fromVisualizationTools.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-10-03
Started: 2024-08-27

Evaluation of Dataset and Marker Gene Alignment

Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga, Ludwig Geistlinger, Robert Gentleman

Rendered fromDatasetMarkerGeneAlignment.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-10-27
Started: 2024-08-27

Detection and Analysis of Annotation Anomalies

Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga, Ludwig Geistlinger, Robert Gentleman

Rendered fromAnnotationAnomalies.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-09-22
Started: 2024-08-27

Readme and manuals

Help Manual

Help pageTopics
Plot Principal Components for Different Cell TypesboxplotPCA
Calculate Categorization EntropycalculateCategorizationEntropy
Function to Calculate Bhattacharyya Coefficients and Hellinger DistancescalculateCellDistancesSimilarity
Calculate Cramer Test P-Values for Two-Sample Comparison of Multivariate ECDFscalculateCramerPValue
Project Query Data onto a Unified Discriminant Space of Reference DatacalculateDiscriminantSpace plot.calculateDiscriminantSpaceObject
Calculate Top Loading Gene Expression ShiftscalculateGeneShifts plot.calculateGeneShiftsObject
Calculate Graph Community Integration DiagnosticscalculateGraphIntegration plot.calculateGraphIntegrationObject
Perform Hotelling's T-squared Test on PCA Scores for Single-cell RNA-seq DatacalculateHotellingPValue
Calculate the Overlap Coefficient for Highly Variable GenescalculateHVGOverlap
Calculate Maximum Mean Discrepancy P-Values for Two-Sample ComparisoncalculateMMDPValue
Calculate Sliced Inverse Regression (SIR) Space for Different Cell TypescalculateSIRSpace plot.calculateSIRSpaceObject
Compare Gene Importance Across Datasets Using Random ForestcalculateVarImpOverlap
Compare Principal Components Analysis (PCA) ResultscomparePCA plot.comparePCAObject
PCA Anomaly Scores via Isolation Forests with VisualizationdetectAnomaly plot.detectAnomalyObject
Histograms: QC Stats and Annotation Scores VisualizationhistQCvsAnnotation
Plot Regression Results on Principal Componentsplot.regressPCObject regressPC
Plot Reference and Query Cell Types using MDSplotCellTypeMDS
Plot Principal Components for Different Cell TypesplotCellTypePCA
Visualize gene expression on a dimensional reduction plotplotGeneExpressionDimred
Visualization of gene sets or pathway scores on dimensional reduction plotplotGeneSetScores
Plot gene expression distribution from overall and cell type-specific perspectiveplotMarkerExpression
Ridgeline Plot of Pairwise Distance AnalysisplotPairwiseDistancesDensity
Scatter plot: QC stats vs Cell Type Annotation ScoresplotQCvsAnnotation
Process PCA for SingleCellExperiment ObjectsprocessPCA
Project Query Data Onto PCA Space of Reference DataprojectPCA
Project Query Data Onto SIR Space of Reference DataprojectSIR