library(spatialDESeq)
se <- make_mock_spatial()
analyzed <- spatialDESeq(se, design = ~ condition, radius = 2.5)
head(SummarizedExperiment::rowData(analyzed))## DataFrame with 6 rows and 3 columns
## spatial_effect_size p_value adjusted_p_value
## <numeric> <numeric> <numeric>
## Gene1 -0.000981879 3.88846e-01 0.670423606
## Gene2 0.048781197 3.09622e-06 0.000154811
## Gene3 0.014807286 2.23815e-01 0.559536761
## Gene4 0.004963442 7.06004e-01 0.840480502
## Gene5 -0.003515539 8.05669e-01 0.875045498
## Gene6 -0.001242366 9.21720e-01 0.921719781## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] spatialDESeq_0.99.2 BiocGenerics_0.59.12 generics_0.1.4
## [4] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.10 SparseArray_1.13.3
## [3] lattice_0.23-1 digest_0.6.39
## [5] magrittr_2.0.5 evaluate_1.0.5
## [7] grid_4.6.1 RColorBrewer_1.1-3
## [9] fastmap_1.2.0 Matrix_1.7-6
## [11] jsonlite_2.0.0 BiocManager_1.30.27
## [13] SingleCellExperiment_1.35.2 scales_1.4.0
## [15] codetools_0.2-20 jquerylib_0.1.4
## [17] abind_1.4-8 cli_3.6.6
## [19] rlang_1.3.0 XVector_0.53.0
## [21] Biobase_2.73.2 DelayedArray_0.39.7
## [23] cachem_1.1.0 yaml_2.3.12
## [25] otel_0.2.0 S4Arrays_1.13.1
## [27] tools_4.6.1 parallel_4.6.1
## [29] BiocParallel_1.47.0 dplyr_1.2.1
## [31] ggplot2_4.0.3 SpatialExperiment_1.23.0
## [33] SummarizedExperiment_1.43.0 buildtools_1.0.0
## [35] vctrs_0.7.3 R6_2.6.1
## [37] magick_2.9.1 matrixStats_1.5.0
## [39] stats4_4.6.1 lifecycle_1.0.5
## [41] Seqinfo_1.3.2 S4Vectors_0.51.10
## [43] IRanges_2.47.5 pkgconfig_2.0.3
## [45] pillar_1.11.1 bslib_0.12.0
## [47] gtable_0.3.6 glue_1.8.1
## [49] Rcpp_1.1.2 xfun_0.61
## [51] tibble_3.3.1 GenomicRanges_1.65.4
## [53] tidyselect_1.2.1 sys_3.4.3
## [55] MatrixGenerics_1.25.0 knitr_1.52
## [57] rjson_0.2.23 farver_2.1.2
## [59] htmltools_0.5.9 rmarkdown_2.32
## [61] maketools_1.3.2 compiler_4.6.1
## [63] S7_0.2.2