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
Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libpng-dev
        libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-14 02:47:24 UTC
RemoteUrl: https://github.com/bioc/wSIR
RemoteRef: HEAD
RemoteSha: 7d58fcbfe33efbd531f2f07809f418f8399e92eb
Packaged: 2026-07-18 11:40:17 UTC; root
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>