4 Session information

Here is the output of sessionInfo() on the system on which this document was compiled:

#> R Under development (unstable) (2024-12-10 r87437)
#> Platform: x86_64-pc-linux-gnu
#> Running under: CentOS Linux 7 (Core)
#> 
#> Matrix products: default
#> BLAS:   /biostack/tools/devtools/R/devel_241212/lib64/R/lib/libRblas.so 
#> LAPACK: /biostack/tools/devtools/R/devel_241212/lib64/R/lib/libRlapack.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: Asia/Shanghai
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] scatterpie_0.2.4            magrittr_2.0.3             
#>  [3] ggplot2_3.5.1               SVP_0.99.0                 
#>  [5] scran_1.35.0                scuttle_1.17.0             
#>  [7] ggsc_1.5.0                  SpatialExperiment_1.17.0   
#>  [9] SingleCellExperiment_1.29.1 SummarizedExperiment_1.37.0
#> [11] Biobase_2.67.0              GenomicRanges_1.59.1       
#> [13] GenomeInfoDb_1.43.2         IRanges_2.41.2             
#> [15] S4Vectors_0.45.2            BiocGenerics_0.53.3        
#> [17] generics_0.1.3              MatrixGenerics_1.19.0      
#> [19] matrixStats_1.4.1           bookdown_0.41              
#> 
#> loaded via a namespace (and not attached):
#>   [1] RcppAnnoy_0.0.22          splines_4.5.0            
#>   [3] later_1.4.1               ggplotify_0.1.2          
#>   [5] tibble_3.2.1              polyclip_1.10-7          
#>   [7] fastDummies_1.7.4         lifecycle_1.0.4          
#>   [9] edgeR_4.5.1               globals_0.16.3           
#>  [11] lattice_0.22-6            MASS_7.3-61              
#>  [13] limma_3.63.2              plotly_4.10.4            
#>  [15] sass_0.4.9                rmarkdown_2.29           
#>  [17] jquerylib_0.1.4           yaml_2.3.10              
#>  [19] metapod_1.15.0            httpuv_1.6.15            
#>  [21] Seurat_5.1.0              sctransform_0.4.1        
#>  [23] spam_2.11-0               sp_2.1-4                 
#>  [25] spatstat.sparse_3.1-0     reticulate_1.40.0        
#>  [27] cowplot_1.1.3             pbapply_1.7-2            
#>  [29] RColorBrewer_1.1-3        abind_1.4-8              
#>  [31] zlibbioc_1.53.0           Rtsne_0.17               
#>  [33] purrr_1.0.2               pracma_2.4.4             
#>  [35] yulab.utils_0.1.8         tweenr_2.0.3             
#>  [37] GenomeInfoDbData_1.2.13   ggrepel_0.9.6            
#>  [39] irlba_2.3.5.1             listenv_0.9.1            
#>  [41] spatstat.utils_3.1-1      tidytree_0.4.6           
#>  [43] goftest_1.2-3             RSpectra_0.16-2          
#>  [45] spatstat.random_3.3-2     dqrng_0.4.1              
#>  [47] fitdistrplus_1.2-1        parallelly_1.40.1        
#>  [49] DelayedMatrixStats_1.29.0 leiden_0.4.3.1           
#>  [51] codetools_0.2-20          DelayedArray_0.33.3      
#>  [53] ggforce_0.4.2             tidyselect_1.2.1         
#>  [55] aplot_0.2.3               UCSC.utils_1.3.0         
#>  [57] farver_2.1.2              ScaledMatrix_1.15.0      
#>  [59] spatstat.explore_3.3-3    jsonlite_1.8.9           
#>  [61] BiocNeighbors_2.1.2       progressr_0.15.1         
#>  [63] ggridges_0.5.6            survival_3.7-0           
#>  [65] tools_4.5.0               treeio_1.31.0            
#>  [67] ggstar_1.0.4              ica_1.0-3                
#>  [69] Rcpp_1.0.13-1             glue_1.8.0               
#>  [71] gridExtra_2.3             SparseArray_1.7.2        
#>  [73] xfun_0.49                 dplyr_1.1.4              
#>  [75] withr_3.0.2               fastmap_1.2.0            
#>  [77] bluster_1.17.0            fansi_1.0.6              
#>  [79] digest_0.6.37             rsvd_1.0.5               
#>  [81] gridGraphics_0.5-1        R6_2.5.1                 
#>  [83] mime_0.12                 colorspace_2.1-1         
#>  [85] scattermore_1.2           tensor_1.5               
#>  [87] spatstat.data_3.1-4       utf8_1.2.4               
#>  [89] tidyr_1.3.1               data.table_1.16.4        
#>  [91] httr_1.4.7                htmlwidgets_1.6.4        
#>  [93] S4Arrays_1.7.1            uwot_0.2.2               
#>  [95] pkgconfig_2.0.3           gtable_0.3.6             
#>  [97] lmtest_0.9-40             XVector_0.47.0           
#>  [99] htmltools_0.5.8.1         dotCall64_1.2            
#> [101] SeuratObject_5.0.2        scales_1.3.0             
#> [103] png_0.1-8                 spatstat.univar_3.1-1    
#> [105] ggfun_0.1.8               knitr_1.49               
#> [107] reshape2_1.4.4            rjson_0.2.23             
#> [109] nlme_3.1-166              cachem_1.1.0             
#> [111] zoo_1.8-12                stringr_1.5.1            
#> [113] KernSmooth_2.23-24        parallel_4.5.0           
#> [115] miniUI_0.1.1.1            pillar_1.9.0             
#> [117] grid_4.5.0                vctrs_0.6.5              
#> [119] RANN_2.6.2                promises_1.3.2           
#> [121] BiocSingular_1.23.0       tidydr_0.0.5             
#> [123] beachmat_2.23.4           xtable_1.8-4             
#> [125] cluster_2.1.8             evaluate_1.0.1           
#> [127] magick_2.8.5              locfit_1.5-9.10          
#> [129] cli_3.6.3                 compiler_4.5.0           
#> [131] rlang_1.1.4               crayon_1.5.3             
#> [133] future.apply_1.11.3       labeling_0.4.3           
#> [135] plyr_1.8.9                fs_1.6.5                 
#> [137] stringi_1.8.4             viridisLite_0.4.2        
#> [139] deldir_2.0-4              BiocParallel_1.41.0      
#> [141] munsell_0.5.1             lazyeval_0.2.2           
#> [143] spatstat.geom_3.3-4       Matrix_1.7-1             
#> [145] RcppHNSW_0.6.0            patchwork_1.3.0          
#> [147] sparseMatrixStats_1.19.0  future_1.34.0            
#> [149] statmod_1.5.0             shiny_1.9.1              
#> [151] ROCR_1.0-11               igraph_2.1.2             
#> [153] RcppParallel_5.1.9        bslib_0.8.0              
#> [155] ggtree_3.15.0             fastmatch_1.1-4          
#> [157] ape_5.8
Chang, Yuzhou, Jixin Liu, Yi Jiang, Anjun Ma, Yao Yu Yeo, Qi Guo, Megan McNutt, et al. 2024. “Graph Fourier Transform for Spatial Omics Representation and Analyses of Complex Organs.” Nature Communications 15 (1): 7467.
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