Package: SVP
Title: Predicting cell states and their variability in single-cell or
        spatial omics data
Version: 1.2.1
Authors@R: c(
  person("Shuangbin", "Xu", email = "xshuangbin@163.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3513-5362")),
  person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-6485-8781")))
Description: SVP uses the distance between cells and cells, features
        and features, cells and features in the space of MCA to build
        nearest neighbor graph, then uses random walk with restart
        algorithm to calculate the activity score of gene sets (such as
        cell marker genes, kegg pathway, go ontology, gene modules,
        transcription factor or miRNA target sets, reactome pathway,
        ...), which is then further weighted using the hypergeometric
        test results from the original expression matrix. To detect the
        spatially or single cell variable gene sets or (other features)
        and the spatial colocalization between the features accurately,
        SVP provides some global and local spatial autocorrelation
        method to identify the spatial variable features. SVP is
        developed based on SingleCellExperiment class, which can be
        interoperable with the existing computing ecosystem.
Depends: R (>= 4.1.0)
Imports: Rcpp, RcppParallel, methods, cli, dplyr, rlang, S4Vectors,
        SummarizedExperiment, SingleCellExperiment, SpatialExperiment,
        BiocGenerics, BiocParallel, fastmatch, pracma, stats, withr,
        Matrix, DelayedMatrixStats, deldir, utils, BiocNeighbors,
        ggplot2, ggstar, ggtree, ggfun
Suggests: rmarkdown, prettydoc, broman, RSpectra, BiasedUrn, knitr, ks,
        igraph, testthat (>= 3.0.0), scuttle, magrittr, DropletUtils,
        tibble, tidyr, harmony, aplot, scales, ggsc, scatterpie, scran,
        scater, STexampleData, ape
License: GPL-3
BugReports: https://github.com/YuLab-SMU/SVP/issues
URL: https://github.com/YuLab-SMU/SVP
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
biocViews: SingleCell, Software, Spatial, Transcriptomics, GeneTarget,
        GeneExpression, GeneSetEnrichment, Transcription, GO, KEGG
SystemRequirements: GNU make
ByteCompile: true
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo (>= 14.0), RcppParallel, RcppEigen,
        dqrng
Config/testthat/edition: 3
LazyData: false
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        make libmagick++-dev gsfonts libicu-dev libpng-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-03 07:07:21 UTC
RemoteUrl: https://github.com/bioc/SVP
RemoteRef: RELEASE_3_22
RemoteSha: 1d706a2d4034d23662114f8d71d8b9076b0e67f8
NeedsCompilation: yes
Packaged: 2025-11-11 18:02:32 UTC; root
Author: Shuangbin Xu [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3513-5362>),
  Guangchuang Yu [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>)
Maintainer: Shuangbin Xu <xshuangbin@163.com>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-12 03:10:49 UTC; windows
Archs: x64
