Package: PhiSpace
Title: Continuous cell state annotation for single-cell and spatial
        omics data
Version: 0.99.0
Authors@R: 
    person("Jiadong", "Mao", , "chiatungmao@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-3818-1981"))
Description: Continuous phenotyping of bulk, single-cell and spatial
        omics data using partial least squares regression. The methods
        are described in Mao et al. (2025)
        <doi:10.1186/s13059-025-03755-8> and Mao et al. (2026)
        <doi:10.1016/j.crmeth.2026.101483>.
License: AGPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.5.0), SummarizedExperiment, SingleCellExperiment,
        SpatialExperiment
Imports: Matrix, methods, BiocParallel, ComplexHeatmap, dplyr, ggplot2,
        ggpubr, irlba, magrittr, plyr, stats, scran, FNN, S4Vectors,
        kerndwd, umap, withr
Suggests: AnnotationDbi, BiocStyle, celldex, cluster, knitr,
        org.Mm.eg.db, pls, rmarkdown, scRNAseq, scuttle, STexampleData,
        testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Software, SingleCell, Spatial, Sequencing, Transcriptomics,
        GeneExpression, CellBiology, Classification, Regression,
        DimensionReduction, Clustering
URL: https://mao-lab-org.github.io/PhiSpace/,
        https://github.com/mao-lab-org/PhiSpace
BugReports: https://github.com/mao-lab-org/PhiSpace/issues
Config/pak/sysreqs: cmake libglpk-dev make libmagick++-dev gsfonts
        libicu-dev libpng-dev libxml2-dev libssl-dev perl python3
        zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-13 02:36:28 UTC
RemoteUrl: https://github.com/BiocStaging/PhiSpace
RemoteRef: HEAD
RemoteSha: 684adb8ae077922f2406cbee6a43ffe17908e3a2
NeedsCompilation: no
Packaged: 2026-10-13 03:48:38 UTC; root
Author: Jiadong Mao [aut, cre] (ORCID: <https://orcid.org/0000-0002-3818-1981>)
Maintainer: Jiadong Mao <chiatungmao@gmail.com>