Package: TweedSpot
Title: Self-Adaptive Spatial Tweedie Models for Spatially Variable Gene
        Detection
Version: 0.99.3
Authors@R: c(
    person("Nalin", "Arora", role = c("aut", "cre"),
           email = "naa4050@med.cornell.edu",
           comment = c(affiliation = "Cornell University",
                       ORCID = "0009-0009-1340-688X")),
    person("Himel", "Mallick", role = "aut",
           email = "him4004@med.cornell.edu",
           comment = c(affiliation = "Cornell University")),
    person("Vivian", "Myers", role = "aut"))
Description: TweedSpot detects spatially variable genes (SVGs) in
        spatially resolved transcriptomics data using self-adaptive
        Tweedie generalized additive models with nonparametric spatial
        smoothing. The method models raw counts directly, avoiding the
        bias introduced by log-transformation, adapts a gene-specific
        Tweedie index parameter to the mean-variance relationship of
        each gene, and offers an optional two-part formulation to
        accommodate excess zeros. Inputs and outputs use the
        SpatialExperiment infrastructure for interoperability with the
        Bioconductor ecosystem.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: mgcv, MatrixGenerics, scran, SpatialExperiment,
        SummarizedExperiment, S4Vectors, BiocParallel, methods, stats,
        withr
Suggests: SpaNorm, STexampleData, testthat (>= 3.0.0), ggplot2,
        patchwork, svglite, Matrix, DelayedArray, knitr, rmarkdown,
        BiocStyle
biocViews: Software, Transcriptomics, GeneExpression, RiboSeq, Spatial,
        Regression, StatisticalMethod, DifferentialExpression,
        QualityControl
URL: https://github.com/mallick-lab/TweedSpot
BugReports: https://github.com/mallick-lab/TweedSpot/issues
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libglpk-dev libmagick++-dev gsfonts libicu-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-14 16:02:04 UTC
RemoteUrl: https://github.com/BiocStaging/TweedSpot
RemoteRef: HEAD
RemoteSha: 7cdedd3c7e9fae4b8fb711b4d6a137a4c2796b8d
NeedsCompilation: no
Packaged: 2026-10-14 18:56:10 UTC; root
Author: Nalin Arora [aut, cre] (affiliation: Cornell University, ORCID:
    <https://orcid.org/0009-0009-1340-688X>),
  Himel Mallick [aut] (affiliation: Cornell University),
  Vivian Myers [aut]
Maintainer: Nalin Arora <naa4050@med.cornell.edu>