Package: wSIR
Type: Package
Title: Weighted Sliced Inverse Regression (wSIR) for supervised
        dimension reduction of spatial transcriptomics and single cell
        gene expression data
Version: 0.99.9
Authors@R: c(
    person("Max", "Woollard", email = "mwoo5086@uni.sydney.edu.au", 
    role = c("aut", "cre"),
    comment=c(ORCID="0009-0000-6319-6926")),
    person("Pratibha", "Panwar", role = c("ctb"), 
    comment = c(ORCID = "0000-0002-7437-7084")),
    person("Linh", "Nghiem", role = c("aut"),
    comment=c(ORCID = "0000-0003-2874-9067")),
    person("Shila", "Ghazanfar", email = "shazanfar@gmail.com", 
    role = c("aut"), comment=c(ORCID="0000-0001-7861-6997"))
    )
Description: Weighted Sliced Inverse Regression (wSIR) is a supervised dimension 
    reduction algorithm for spatial transcriptomics gene expression data. For a 
    provided gene expression matrix and dataframe of each cell's spatial 
    coordinates, wSIR creates a low-dimensional representation of the gene 
    expression data that preserves the ability to predict spatial coordinates 
    that was present in the gene expression data. Furthermore, wSIR provides 
    interpretable loadings which allow for projection of new single-cell gene 
    expression data into a low-dimensional space which preserves the spatial 
    information present in the gene expression data.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://sydneybiox.github.io/wSIR,
        https://github.com/SydneyBioX/wSIR
BugReports: https://github.com/sydneybiox/wSIR/issues
biocViews: DimensionReduction, Software, GeneExpression, SingleCell,
        Spatial, Transcriptomics, Regression, CellBasedAssays
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.4.0),
Imports: magrittr (>= 2.0) , ggplot2 (>= 3.5.1), umap (>= 0.2.10),
        vctrs (>= 0.6), stringr (>= 1.5.1), distances (>= 0.1.11), Rcpp
        (>= 1.0.11), doBy (>= 4.6.0), BiocParallel (>= 1.38.0), rlang,
        methods, BiocGenerics (>= 0.50.0), SummarizedExperiment (>=
        1.34.0), SingleCellExperiment (>= 1.26.0), SpatialExperiment
        (>= 1.14.0)
Suggests: knitr, BiocStyle, class, testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
RoxygenNote: 7.3.3
NeedsCompilation: yes
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/wSIR
git_branch: devel
git_last_commit: 7d58fcb
git_last_commit_date: 2026-07-13
Repository: Bioconductor 3.24
Date/Publication: 2026-07-16
Packaged: 2026-07-16 23:04:17 UTC; biocbuild
Author: Max Woollard [aut, cre] (ORCID:
    <https://orcid.org/0009-0000-6319-6926>),
  Pratibha Panwar [ctb] (ORCID: <https://orcid.org/0000-0002-7437-7084>),
  Linh Nghiem [aut] (ORCID: <https://orcid.org/0000-0003-2874-9067>),
  Shila Ghazanfar [aut] (ORCID: <https://orcid.org/0000-0001-7861-6997>)
Maintainer: Max Woollard <mwoo5086@uni.sydney.edu.au>
Built: R 4.6.1; x86_64-apple-darwin20; 2026-07-17 05:57:14 UTC; unix
