Package: SpaGER
Type: Package
Title: Spatial Gene Expression Prediction using scRNA-seq
Version: 1.0.0
Date: 2026-01-25
Author: Zaoqu Liu [aut, cre] (<https://orcid.org/0000-0002-0452-742X>),
        Tamim Abdelaal [ctb] (Original SpaGE algorithm), Soufiane
        Mourragui [ctb] (PRECISE algorithm)
Maintainer: Zaoqu Liu <liuzaoqu@163.com>
Authors@R: c(
    person("Zaoqu", "Liu", email = "liuzaoqu@163.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0452-742X")),
    person("Tamim", "Abdelaal", role = "ctb",
           comment = "Original SpaGE algorithm"),
    person("Soufiane", "Mourragui", role = "ctb",
           comment = "PRECISE algorithm")
    )
Description: Integrates spatial transcriptomics data with single-cell
        RNA sequencing (scRNA-seq) data to predict expression of
        unmeasured genes in spatial data. Uses Principal Vectors (PVs)
        for domain adaptation followed by k-nearest neighbor weighted
        imputation. This R implementation provides identical results to
        the original Python SpaGE package with efficient C++
        acceleration.
License: MIT + file LICENSE
URL: https://github.com/Zaoqu-Liu/SpaGER
BugReports: https://github.com/Zaoqu-Liu/SpaGER/issues
Encoding: UTF-8
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.0.0)
Imports: stats, Matrix, methods, Rcpp (>= 1.0.0), irlba, FNN, parallel,
        future, future.apply, MASS
Suggests: Seurat (>= 4.0.0), SeuratObject, fastICA, NMF, pls, psych,
        testthat (>= 3.0.0), knitr, rmarkdown, ggplot2
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: yes
SystemRequirements: C++
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-24 17:55:59 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/SpaGER
RemoteRef: main
RemoteSha: fa7fc0afbd10efeadfacc48984d5a253d375aff9
Packaged: 2026-06-23 07:46:28 UTC; root