Package: SPOTlight
Version: 1.12.1
Type: Package
Title: `SPOTlight`: Spatial Transcriptomics Deconvolution
Description: `SPOTlight` provides a method to deconvolute spatial transcriptomics
    spots using a seeded NMF approach along with visualization tools to assess
    the results. Spatially resolved gene expression profiles are key to
    understand tissue organization and function. However, novel spatial 
    transcriptomics (ST) profiling techniques lack single-cell resolution and 
    require a combination with single-cell RNA sequencing (scRNA-seq) 
    information to deconvolute the spatially indexed datasets. Leveraging the 
    strengths of both data types, we developed SPOTlight, a computational tool 
    that enables the integration of ST with scRNA-seq data to infer the location
    of cell types and states within a complex tissue. SPOTlight is centered 
    around a seeded non-negative matrix factorization (NMF) regression, 
    initialized using cell-type marker genes and non-negative least squares
    (NNLS) to subsequently deconvolute ST capture locations (spots).
Authors@R: c(
  person("Marc", "Elosua-Bayes", email="elosua.marc@gmail.com", role=c("aut", "cre")),
  person("Zachary", "DeBruine", email="zacharydebruine@gmail.com", role="aut"),
  person("Helena L.", "Crowell", email="helena@crowell.eu", role="aut"))
Depends: R (>= 4.1)
Imports: ggplot2, Matrix, SingleCellExperiment, sparseMatrixStats,
        stats
Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils,
        ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg,
        knitr, methods, png, rmarkdown, scater, scatterpie, scran,
        SpatialExperiment, SummarizedExperiment, S4Vectors,
        TabulaMurisSenisData, TENxVisiumData, testthat
LinkingTo: Rcpp, RcppEigen
biocViews: SingleCell, Spatial, StatisticalMethod
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/MarcElosua/SPOTlight
BugReports: https://github.com/MarcElosua/SPOTlight/issues
git_url: https://git.bioconductor.org/packages/SPOTlight
git_branch: RELEASE_3_21
git_last_commit: 55527f6
git_last_commit_date: 2025-05-26
Repository: Bioconductor 3.21
Date/Publication: 2025-05-29
NeedsCompilation: yes
Packaged: 2025-05-30 02:35:04 UTC; biocbuild
Author: Marc Elosua-Bayes [aut, cre],
  Zachary DeBruine [aut],
  Helena L. Crowell [aut]
Maintainer: Marc Elosua-Bayes <elosua.marc@gmail.com>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-05-30 14:19:11 UTC; windows
Archs: x64
