Type: Package
Package: scDiagnostics
Title: Cell type annotation diagnostics
Version: 1.4.0
Authors@R: c(
    person("Anthony", "Christidis", role = c("aut", "cre"), 
            email = "anthony-alexander_christidis@hms.harvard.edu", 
            comment = c(ORCID = "0000-0002-4565-6279")),
    person("Andrew", "Ghazi", role = "aut"),
    person("Smriti", "Chawla", role = "aut"),
    person("Nitesh", "Turaga", role = "ctb"),
    person("Ludwig", "Geistlinger", role = "aut"),
    person("Robert", "Gentleman", role = "aut")
  )
Description: 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.
License: Artistic-2.0
URL: https://github.com/ccb-hms/scDiagnostics
BugReports: https://github.com/ccb-hms/scDiagnostics/issues
Depends: R (>= 4.4.0)
Imports: SingleCellExperiment, methods, isotree, FNN, igraph, ggplot2,
        GGally, ggridges, SummarizedExperiment, ranger, transport,
        cramer, rlang, bluster, scales, MASS, stringr, Matrix,
        grDevices
Suggests: AUCell, BiocStyle, knitr, rmarkdown, scran, scRNAseq,
        SingleR, celldex, scuttle, scater, dplyr, ComplexHeatmap, grid,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: Annotation, Classification, Clustering, GeneExpression,
        RNASeq, SingleCell, Software, Transcriptomics
Encoding: UTF-8
LazyDataCompression: xz
RoxygenNote: 7.3.2
Config/testthat/edition: 3
LazyData: true
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:31:45 UTC
RemoteUrl: https://github.com/bioc/scDiagnostics
RemoteRef: RELEASE_3_22
RemoteSha: 7dca06163b8a28ef4c0ff0631bdc61c3b8638d37
NeedsCompilation: no
Packaged: 2026-01-24 21:14:43 UTC; root
Author: Anthony Christidis [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4565-6279>),
  Andrew Ghazi [aut],
  Smriti Chawla [aut],
  Nitesh Turaga [ctb],
  Ludwig Geistlinger [aut],
  Robert Gentleman [aut]
Maintainer: Anthony Christidis <anthony-alexander_christidis@hms.harvard.edu>
Built: R 4.5.2; ; 2026-01-24 21:18:35 UTC; windows
