Package: spatialDESeq Title: Spatial Differential Expression via Spatial Autoregressive GLMs Version: 0.99.2 Authors@R: person("Sahal", "Paladan", email = "sahalpaladan@gmail.com", role = c("aut", "cre")) Description: A robust, parallelized statistical framework optimized for identifying spatially differential expression in high-throughput spatial transcriptomics datasets. The package extends standard negative binomial generalized linear models (GLMs) by incorporating continuous physical tissue spot coordinates as distance-weighted local smoothing covariates. This configuration models spatial context seamlessly without relying on pre-annotated categorical tissue clusters. The underlying distance matrix evaluations and coordinate smoothing routines are accelerated natively via an optimized C++ Armadillo matrix engine to guarantee computational efficiency. Built to integrate natively into the Bioconductor ecosystem, the package operates directly on SpatialExperiment containers, incorporates robust library-size normalization scaling factor offsets, calculates adjusted p-values for multi-gene profiles, and supplies an interactive Shiny-based point-and-click visualization dashboard tool for downstream exploratory data analysis. License: MIT + file LICENSE Encoding: UTF-8 biocViews: GeneExpression, RNASeq, Sequencing, Spatial, Transcriptomics, DifferentialExpression, Software URL: https://github.com BugReports: https://github.com/issues Depends: R (>= 4.4.0), BiocGenerics Imports: methods, SpatialExperiment (>= 1.12.0), SummarizedExperiment (>= 1.32.0), BiocParallel (>= 1.36.0), Rcpp (>= 1.0.11), ggplot2 (>= 3.4.0), stats LinkingTo: Rcpp, RcppArmadillo (>= 0.12.0) Suggests: testthat (>= 3.0.0), shiny (>= 1.8.0), BiocStyle (>= 2.30.0), knitr (>= 1.45), rmarkdown (>= 2.25) VignetteBuilder: knitr Config/roxygen2/version: 8.0.0 Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libssl-dev zlib1g-dev Repository: https://biocstaging.r-universe.dev Date/Publication: 2026-08-24 10:16:58 UTC RemoteUrl: https://github.com/BiocStaging/spatialDESeq RemoteRef: HEAD RemoteSha: 4ad1683a4f1a2d30f88bc6adf7ca93d87adb09b1 NeedsCompilation: yes Packaged: 2026-09-23 11:30:28 UTC; root Author: Sahal Paladan [aut, cre] Maintainer: Sahal Paladan