Hi,
Thank you for the nice tool! We are recently using nnSVG to discover the spatial variable genes from Xenium data.
However, it has been running for over 12 hours without any errors, and we're unsure if this is expected behavior.
Our object is
> spe
class: SpatialExperiment
dim: 90 208867
metadata(0):
assays(3): counts logcounts scaledata
rownames(90): ACE2 ACTG2 ... VEGFA VWA5A
rowData names(1): gene_name
colnames(208867): aaabnalk-1 aaabojfc-1 ... oijbgikh-1 oijcflhj-1
colData names(20): orig.ident nCount_Xenium.with.snvs ... ident
sample_id
reducedDimNames(2): PCA UMAP.30PC
mainExpName: NULL
altExpNames(5): Xenium.with.snvs BlankCodeword ControlCodeword
ControlProbe Xenium
spatialCoords names(2) : x y
imgData names(0):
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: ~/envs/scenv/lib/libopenblasp-r0.3.27.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: America/Chicago
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_3.5.1 scran_1.30.2
[3] scuttle_1.12.0 nnSVG_1.6.4
[5] SPARK_1.1.1 stringr_1.5.1
[7] dplyr_1.1.4 SpatialExperiment_1.12.0
[9] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
[11] Biobase_2.62.0 GenomicRanges_1.54.1
[13] GenomeInfoDb_1.38.1 IRanges_2.36.0
[15] S4Vectors_0.40.2 BiocGenerics_0.48.1
[17] MatrixGenerics_1.14.0 matrixStats_1.4.1
[19] Seurat_5.1.0 SeuratObject_5.0.2
[21] sp_2.1-4
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.3.3
[3] later_1.3.2 bitops_1.0-8
[5] tibble_3.2.1 polyclip_1.10-7
[7] matlab_1.0.4.1 fastDummies_1.7.4
[9] lifecycle_1.0.4 edgeR_3.42.4
[11] doParallel_1.0.17 globals_0.16.3
[13] processx_3.8.4 lattice_0.22-6
[15] MASS_7.3-60.0.1 magrittr_2.0.3
[17] limma_3.58.1 plotly_4.10.4
[19] remotes_2.5.0 metapod_1.10.1
[21] httpuv_1.6.15 sctransform_0.4.1
[23] spam_2.10-0 sessioninfo_1.2.2
[25] pkgbuild_1.4.4 spatstat.sparse_3.1-0
[27] reticulate_1.39.0 cowplot_1.1.3
[29] pbapply_1.7-2 RColorBrewer_1.1-3
[31] abind_1.4-5 pkgload_1.4.0
[33] zlibbioc_1.48.0 Rtsne_0.17
[35] purrr_1.0.2 RCurl_1.98-1.16
[37] pracma_2.4.4 GenomeInfoDbData_1.2.11
[39] ggrepel_0.9.6 irlba_2.3.5.1
[41] listenv_0.9.1 spatstat.utils_3.1-0
[43] goftest_1.2-3 RSpectra_0.16-2
[45] dqrng_0.3.2 spatstat.random_3.2-3
[47] fitdistrplus_1.2-1 parallelly_1.38.0
[49] DelayedMatrixStats_1.24.0 leiden_0.4.3.1
[51] codetools_0.2-20 DelayedArray_0.28.0
[53] tidyselect_1.2.1 farver_2.1.2
[55] ScaledMatrix_1.10.0 spatstat.explore_3.2-6
[57] jsonlite_1.8.8 BiocNeighbors_1.20.0
[59] ellipsis_0.3.2 progressr_0.14.0
[61] ggridges_0.5.6 survival_3.7-0
[63] iterators_1.0.14 systemfonts_1.1.0
[65] foreach_1.5.2 tools_4.3.3
[67] ragg_1.3.2 ica_1.0-3
[69] Rcpp_1.0.13 glue_1.7.0
[71] gridExtra_2.3 SparseArray_1.2.2
[73] usethis_3.0.0 withr_3.0.1
[75] fastmap_1.2.0 bluster_1.12.0
[77] fansi_1.0.6 rsvd_1.0.5
[79] callr_3.7.6 digest_0.6.37
[81] R6_2.5.1 mime_0.12
[83] textshaping_0.4.0 colorspace_2.1-1
[85] scattermore_1.2 tensor_1.5
[87] spatstat.data_3.1-2 utf8_1.2.4
[89] tidyr_1.3.1 generics_0.1.3
[91] data.table_1.15.4 httr_1.4.7
[93] htmlwidgets_1.6.4 S4Arrays_1.2.0
[95] uwot_0.1.16 pkgconfig_2.0.3
[97] gtable_0.3.5 rdist_0.0.5
[99] BRISC_1.0.6 lmtest_0.9-40
[101] XVector_0.42.0 htmltools_0.5.8.1
[103] profvis_0.3.8 dotCall64_1.1-1
[105] scales_1.3.0 png_0.1-8
[107] reshape2_1.4.4 rjson_0.2.21
[109] nlme_3.1-165 curl_5.2.1
[111] cachem_1.1.0 zoo_1.8-12
[113] KernSmooth_2.23-24 parallel_4.3.3
[115] miniUI_0.1.1.1 desc_1.4.3
[117] pillar_1.9.0 grid_4.3.3
[119] vctrs_0.6.5 RANN_2.6.2
[121] urlchecker_1.0.1 promises_1.3.0
[123] BiocSingular_1.18.0 beachmat_2.18.0
[125] xtable_1.8-4 cluster_2.1.6
[127] magick_2.8.5 locfit_1.5-9.10
[129] cli_3.6.3 compiler_4.3.3
[131] rlang_1.1.4 crayon_1.5.3
[133] future.apply_1.11.2 labeling_0.4.3
[135] ps_1.7.7 plyr_1.8.9
[137] fs_1.6.4 stringi_1.8.4
[139] BiocParallel_1.36.0 viridisLite_0.4.2
[141] deldir_2.0-4 munsell_0.5.1
[143] lazyeval_0.2.2 devtools_2.4.5
[145] spatstat.geom_3.2-9 CompQuadForm_1.4.3
[147] Matrix_1.6-5 RcppHNSW_0.6.0
[149] patchwork_1.2.0 sparseMatrixStats_1.14.0
[151] future_1.34.0 statmod_1.5.0
[153] shiny_1.9.1 ROCR_1.0-11
[155] igraph_2.0.3 memoise_2.0.1
Hi,
Thank you for the nice tool! We are recently using nnSVG to discover the spatial variable genes from Xenium data.
However, it has been running for over 12 hours without any errors, and we're unsure if this is expected behavior.
Our object is