Package: scDiagnostics 0.99.11

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_0.99.11.tar.gz
scDiagnostics_0.99.11.zip(r-4.5)scDiagnostics_0.99.11.zip(r-4.4)scDiagnostics_0.99.10.zip(r-4.3)
scDiagnostics_0.99.11.tgz(r-4.4-any)scDiagnostics_0.99.10.tgz(r-4.3-any)
scDiagnostics_0.99.11.tar.gz(r-4.5-noble)scDiagnostics_0.99.11.tar.gz(r-4.4-noble)
scDiagnostics_0.99.11.tgz(r-4.4-emscripten)scDiagnostics_0.99.10.tgz(r-4.3-emscripten)
scDiagnostics.pdf |scDiagnostics.html
scDiagnostics/json (API)
NEWS

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

Peer review:

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

Datasets:

    On BioConductor:scDiagnostics-0.99.10(bioc 3.20)

    annotationclassificationclusteringgeneexpressionrnaseqsinglecellsoftwaretranscriptomics

    7.37 score 3 stars 54 scripts 29 exports 81 dependencies

    Last updated 5 days agofrom:c58572e51c. Checks:OK: 1 ERROR: 1 NOTE: 5. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKOct 26 2024
    R-4.5-winNOTEOct 26 2024
    R-4.5-linuxNOTEOct 26 2024
    R-4.4-winNOTEOct 26 2024
    R-4.4-macNOTEOct 26 2024
    R-4.3-winNOTESep 26 2024
    R-4.3-macERRORSep 26 2024

    Exports:boxplotPCAcalculateAveragePairwiseCorrelationcalculateCategorizationEntropycalculateCellDistancescalculateCellDistancesSimilaritycalculateCellSimilarityPCAcalculateCramerPValuecalculateDiscriminantSpacecalculateHotellingPValuecalculateHVGOverlapcalculateNearestNeighborProbabilitiescalculateSIRSpacecalculateVarImpOverlapcalculateWassersteinDistancecompareCCAcomparePCAcomparePCASubspacedetectAnomalyhistQCvsAnnotationplotCellTypeMDSplotCellTypePCAplotGeneExpressionDimredplotGeneSetScoresplotMarkerExpressionplotPairwiseDistancesDensityplotQCvsAnnotationprojectPCAprojectSIRregressPC

    Dependencies:abindaskpassassortheadBHbiglmBiobaseBiocGenericsBiocNeighborsBiocParallelblusterbootcliclustercodetoolscolorspacecpp11cramercrayoncurldata.tableDBIDelayedArrayfansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggridgesgluegtablehttrigraphIRangesisobandisotreejsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigR6rangerRColorBrewerRcppRcppEigenrlangS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArrayspeedglmSummarizedExperimentsystibbletransportUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

    Getting Started with scDiagnostics

    Rendered fromscDiagnostics.Rmdusingknitr::rmarkdownon Oct 26 2024.

    Last update: 2024-10-25
    Started: 2023-08-04

    Visualization of Cell Type Annotations

    Rendered fromVisualizationTools.Rmdusingknitr::rmarkdownon Oct 26 2024.

    Last update: 2024-10-25
    Started: 2024-08-27

    Evaluation of Dataset and Marker Gene Alignment

    Rendered fromDatasetMarkerGeneAlignment.Rmdusingknitr::rmarkdownon Oct 26 2024.

    Last update: 2024-10-25
    Started: 2024-08-27

    Detection and Analysis of Annotation Anomalies

    Rendered fromAnnotationAnomalies.Rmdusingknitr::rmarkdownon Oct 26 2024.

    Last update: 2024-10-25
    Started: 2024-08-27