Preface
This is a Quarto book of code accompanying our manuscript “A clinically relevant spatial single-cell landscape of pancreatic cancer”.
R version 4.4.1 (2024-06-14)
Platform: x86_64-conda-linux-gnu
Running under: CentOS Linux 8
Matrix products: default
BLAS/LAPACK: /cluster/apps/anaconda3/2020.02/envs/R-4.4.1/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: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ggraph_2.2.1 tidygraph_1.3.1
[3] ggrepel_0.9.6 viridis_0.6.5
[5] viridisLite_0.4.2 jhuanglabRNAseq_1.0.0
[7] SummarizedExperiment_1.36.0 Biobase_2.66.0
[9] GenomicRanges_1.58.0 GenomeInfoDb_1.42.1
[11] IRanges_2.40.1 S4Vectors_0.44.0
[13] BiocGenerics_0.52.0 MatrixGenerics_1.18.1
[15] matrixStats_1.5.0 ComplexHeatmap_2.22.0
[17] circlize_0.4.16 lubridate_1.9.4
[19] forcats_1.0.0 stringr_1.5.1
[21] dplyr_1.1.4 purrr_1.0.4
[23] readr_2.1.5 tidyr_1.3.1
[25] tibble_3.2.1 ggplot2_3.5.1
[27] tidyverse_2.0.0 patchwork_1.3.0
[29] ggsci_3.2.0 glue_1.8.0
[31] jhtools_1.0.0 ggthemes_5.1.0
loaded via a namespace (and not attached):
[1] fs_1.6.5 easySVG_0.1.0 bitops_1.0-9
[4] enrichplot_1.26.6 httr_1.4.7 RColorBrewer_1.1-3
[7] doParallel_1.0.17 tools_4.4.1 backports_1.5.0
[10] R6_2.5.1 lazyeval_0.2.2 GetoptLong_1.0.5
[13] withr_3.0.2 prettyunits_1.2.0 gridExtra_2.3
[16] cli_3.6.3 formatR_1.14 genefilter_1.88.0
[19] ngstk_0.2.3 ggridges_0.5.6 Rsamtools_2.22.0
[22] yulab.utils_0.1.9 gson_0.1.0 DOSE_4.0.0
[25] R.utils_2.12.3 ini_0.3.1 parallelly_1.41.0
[28] limma_3.62.2 RSQLite_2.3.9 BiocIO_1.16.0
[31] generics_0.1.3 gridGraphics_0.5-1 shape_1.4.6.1
[34] configr_0.3.5 hwriter_1.3.2.1 gtools_3.9.5
[37] car_3.1-3 zip_2.3.1 dendextend_1.19.0
[40] GO.db_3.20.0 Matrix_1.7-1 futile.logger_1.4.3
[43] abind_1.4-8 R.methodsS3_1.8.2 lifecycle_1.0.4
[46] yaml_2.3.10 carData_3.0-5 gplots_3.2.0
[49] qvalue_2.38.0 SparseArray_1.6.1 BiocFileCache_2.14.0
[52] blob_1.2.4 gdata_3.0.1 crayon_1.5.3
[55] RcppTOML_0.2.2 ggtangle_0.0.6 lattice_0.22-6
[58] msigdbr_7.5.1 cowplot_1.1.3 annotate_1.84.0
[61] KEGGREST_1.46.0 pillar_1.10.1 knitr_1.49
[64] optparse_1.7.5 fgsea_1.32.2 rjson_0.2.23
[67] codetools_0.2-20 fastmatch_1.1-6 ggfun_0.1.8
[70] data.table_1.16.4 vctrs_0.6.5 png_0.1-8
[73] treeio_1.30.0 gtable_0.3.6 cachem_1.1.0
[76] xfun_0.50 openxlsx_4.2.7.1 S4Arrays_1.6.0
[79] survival_3.8-3 iterators_1.0.14 statmod_1.5.0
[82] nlme_3.1-166 ggtree_3.14.0 bit64_4.6.0-1
[85] progress_1.2.3 filelock_1.0.3 KernSmooth_2.23-26
[88] colorspace_2.1-1 DBI_1.2.3 DESeq2_1.46.0
[91] tidyselect_1.2.1 bit_4.5.0.1 compiler_4.4.1
[94] curl_6.1.0 httr2_1.1.0 xml2_1.3.6
[97] DelayedArray_0.32.0 rtracklayer_1.66.0 scales_1.3.0
[100] caTools_1.18.3 rappdirs_0.3.3 digest_0.6.37
[103] rmarkdown_2.29 XVector_0.46.0 htmltools_0.5.8.1
[106] pkgconfig_2.0.3 gvmap_0.1.6 dbplyr_2.5.0
[109] fastmap_1.2.0 rlang_1.1.5 GlobalOptions_0.1.2
[112] htmlwidgets_1.6.4 UCSC.utils_1.2.0 farver_2.1.2
[115] jsonlite_1.8.9 DEXSeq_1.52.0 BiocParallel_1.40.0
[118] GOSemSim_2.32.0 R.oo_1.27.0 RCurl_1.98-1.16
[121] magrittr_2.0.3 Formula_1.2-5 GenomeInfoDbData_1.2.13
[124] ggplotify_0.1.2 munsell_0.5.1 Rcpp_1.0.14
[127] ape_5.8-1 babelgene_22.9 stringi_1.8.4
[130] MASS_7.3-64 zlibbioc_1.52.0 plyr_1.8.9
[133] org.Hs.eg.db_3.20.0 parallel_4.4.1 listenv_0.9.1
[136] graphlayouts_1.2.1 Biostrings_2.74.1 splines_4.4.1
[139] hms_1.1.3 locfit_1.5-9.10 igraph_2.1.3
[142] ggpubr_0.6.0 ggsignif_0.6.4 reshape2_1.4.4
[145] geneplotter_1.84.0 biomaRt_2.62.0 futile.options_1.0.1
[148] XML_3.99-0.18 evaluate_1.0.3 lambda.r_1.2.4
[151] tweenr_2.0.3 tzdb_0.4.0 foreach_1.5.2
[154] polyclip_1.10-7 getopt_1.20.4 future_1.34.0
[157] clue_0.3-66 ggforce_0.4.2 broom_1.0.7
[160] xtable_1.8-4 restfulr_0.0.15 rsvg_2.6.0
[163] tidytree_0.4.6 rstatix_0.7.2 clusterProfiler_4.14.4
[166] aplot_0.2.4 GenomicAlignments_1.42.0 memoise_2.0.1
[169] AnnotationDbi_1.68.0 tximport_1.34.0 cluster_2.1.8
[172] corrplot_0.95 timechange_0.3.0 globals_0.16.3
[175] ggfortify_0.4.17