sessionInfo # R version 4.4.2 (2024-10-31) # Platform: x86_64-pc-linux-gnu # Running under: Ubuntu 20.04.6 LTS # # Matrix products: default # BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 # LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 # # 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 grid stats graphics grDevices utils datasets # [8] methods base # # other attached packages: # [1] icellnet_2.2.1 jetset_3.4.0 hgu133plus2.db_3.13.0 # [4] org.Hs.eg.db_3.16.0 AnnotationDbi_1.68.0 IRanges_2.32.0 # [7] S4Vectors_0.36.0 devtools_2.4.5 usethis_2.1.6 # [10] magrittr_2.0.3 networkD3_0.4 pheatmap_1.0.12 # [13] cellcall_1.0.7 RColorBrewer_1.1-3 forcats_1.0.0 # [16] stringr_1.5.1 purrr_1.0.2 readr_2.1.5 # [19] tidyr_1.3.1 tibble_3.2.1 tidyverse_1.3.2 # [22] Seurat_5.0.3 SeuratObject_5.0.1 sp_2.1-4 # [25] nichenetr_2.2.0 ComplexHeatmap_2.14.0 cowplot_1.1.3 # [28] ggalluvial_0.12.5 patchwork_1.3.0 CellChat_1.6.1 # [31] bigmemory_4.6.4 Biobase_2.66.0 BiocGenerics_0.52.0 # [34] ggplot2_3.5.1 igraph_2.0.1.1 dplyr_1.1.4 # # loaded via a namespace (and not attached): # [1] ica_1.0-3 plotly_4.10.1 Formula_1.2-5 # [4] zlibbioc_1.52.0 tidyselect_1.2.1 rvest_1.0.3 # [7] bit_4.5.0.1 doParallel_1.0.17 clue_0.3-66 # [10] lattice_0.22-6 rjson_0.2.23 urlchecker_1.0.1 # [13] blob_1.2.4 rngtools_1.5.2 parallel_4.4.2 # [16] caret_6.0-93 png_0.1-8 cli_3.6.3 # [19] ggplotify_0.1.0 usdata_0.3.1 registry_0.5-1 # [22] goftest_1.2-3 gargle_1.2.1 textshaping_0.3.6 # [25] BiocNeighbors_2.0.1 ggnetwork_0.5.13 uwot_0.1.14 # [28] shadowtext_0.1.4 mime_0.12 evaluate_1.0.3 # [31] tidytree_0.4.1 leiden_0.4.3 openintro_2.4.0 # [34] stringi_1.8.4 pROC_1.18.0 backports_1.5.0 # [37] lubridate_1.9.0 httpuv_1.6.6 clusterProfiler_4.6.0 # [40] splines_4.4.2 prodlim_2019.11.13 jpeg_0.1-10 # [43] ggraph_2.1.0 DT_0.26 sctransform_0.4.1 # [46] ggbeeswarm_0.7.2 sessioninfo_1.2.2 DBI_1.2.3 # [49] jquerylib_0.1.4 withr_3.0.2 class_7.3-20 # [52] systemfonts_1.1.0 enrichplot_1.18.1 lmtest_0.9-40 # [55] ggnewscale_0.5.0 tidygraph_1.2.2 BiocManager_1.30.25 # [58] htmlwidgets_1.5.4 fs_1.6.5 ggrepel_0.9.6 # [61] cherryblossom_0.1.0 statnet.common_4.11.0 labeling_0.4.3 # [64] cellranger_1.1.0 reticulate_1.26 zoo_1.8-12 # [67] XVector_0.38.0 knitr_1.49 network_1.18.0 # [70] airports_0.1.0 timechange_0.3.0 foreach_1.5.2 # [73] caTools_1.18.3 visNetwork_2.1.2 data.table_1.16.4 # [76] timeDate_4041.110 ggtree_3.6.2 psych_2.4.12 # [79] RSpectra_0.16-2 irlba_2.3.5.1 DiagrammeR_1.0.11 # [82] ggrastr_1.0.1 fastDummies_1.7.4 gridGraphics_0.5-1 # [85] ellipsis_0.3.2 lazyeval_0.2.2 yaml_2.3.10 # [88] survival_3.4-0 scattermore_1.2 crayon_1.5.3 # [91] RcppAnnoy_0.0.22 progressr_0.15.1 tweenr_2.0.3 # [94] later_1.4.1 profvis_0.3.7 ggridges_0.5.6 # [97] codetools_0.2-20 base64enc_0.1-3 GlobalOptions_0.1.2 # [100] KEGGREST_1.38.0 Rtsne_0.17 shape_1.4.6.1 # [103] limma_3.62.2 foreign_0.8-88 pkgconfig_2.0.3 # [106] xml2_1.3.6 ggpubr_0.5.0 aplot_0.1.8 # [109] spatstat.sparse_3.1-0 ape_5.8-1 viridisLite_0.4.2 # [112] gridBase_0.4-7 xtable_1.8-4 interp_1.1-6 # [115] car_3.1-1 plyr_1.8.9 httr_1.4.4 # [118] tools_4.4.2 globals_0.16.3 hardhat_1.4.0 # [121] pkgbuild_1.3.1 beeswarm_0.4.0 htmlTable_2.4.1 # [124] broom_1.0.7 checkmate_2.3.2 nlme_3.1-160 # [127] HDO.db_0.99.1 dbplyr_2.5.0 crosstalk_1.2.1 # [130] digest_0.6.37 Matrix_1.7-1 farver_2.1.2 # [133] tzdb_0.4.0 reshape2_1.4.4 ModelMetrics_1.2.2.2 # [136] yulab.utils_0.1.9 viridis_0.6.5 rpart_4.1.24 # [139] glue_1.8.0 cachem_1.1.0 polyclip_1.10-7 # [142] Hmisc_4.7-2 generics_0.1.3 Biostrings_2.66.0 # [145] googledrive_2.0.0 presto_1.0.0 parallelly_1.41.0 # [148] pkgload_1.4.0 mnormt_2.1.1 statmod_1.5.0 # [151] RcppHNSW_0.6.0 ragg_1.4.0 carData_3.0-5 # [154] pbapply_1.7-2 spam_2.11-0 gson_0.1.0 # [157] utf8_1.2.4 gower_1.0.2 graphlayouts_0.8.3 # [160] readxl_1.4.3 ggsignif_0.6.4 gridExtra_2.3 # [163] shiny_1.10.0 lava_1.7.0 GenomeInfoDbData_1.2.13 # [166] RCurl_1.98-1.16 memoise_2.0.1 rmarkdown_2.29 # [169] downloader_0.4 scales_1.3.0 googlesheets4_1.0.1 # [172] future_1.34.0 svglite_2.1.0 RANN_2.6.2 # [175] Cairo_1.6-2 bigmemory.sri_0.1.8 spatstat.data_3.1-4 # [178] rstudioapi_0.17.1 cluster_2.1.8 spatstat.utils_3.1-2 # [181] hms_1.1.3 fitdistrplus_1.2-2 munsell_0.5.1 # [184] fdrtool_1.2.18 colorspace_2.1-1 FNN_1.1.4.1 # [187] rlang_1.1.4 GenomeInfoDb_1.34.3 ipred_0.9-13 # [190] dotCall64_1.2 ggforce_0.4.2 circlize_0.4.16 # [193] xfun_0.50 coda_0.19-4.1 e1071_1.7-16 # [196] sna_2.7-2 modelr_0.1.10 remotes_2.5.0 # [199] recipes_1.0.3 iterators_1.0.14 matrixStats_1.5.0 # [202] abind_1.4-8 randomForest_4.7-1.2 GOSemSim_2.24.0 # [205] treeio_1.22.0 bitops_1.0-9 ps_1.8.1 # [208] promises_1.3.2 scatterpie_0.1.8 RSQLite_2.3.9 # [211] qvalue_2.38.0 reprex_2.0.2 fgsea_1.24.0 # 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