Chapter 24 Session Information
This tutorial was run on the date specified below.
## [1] "2025-02-06"The sessionInfo() at run time was:
sessionInfo()
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 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-r0.3.20.so; LAPACK version 3.10.0
##
## Random number generation:
## RNG: L'Ecuyer-CMRG
## Normal: Inversion
## Sample: Rejection
##
## 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] parallel stats4 grid stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] zlibbioc_1.50.0
## [2] zip_2.3.1
## [3] yaml_2.3.10
## [4] xtable_1.8-4
## [5] xopen_1.0.1
## [6] xml2_1.3.6
## [7] xfun_0.48
## [8] wk_0.9.4
## [9] withr_3.0.2
## [10] whisker_0.4.1
## [11] warp_0.2.1
## [12] waldo_0.5.3
## [13] vroom_1.6.5
## [14] viridis_0.6.5
## [15] viridisLite_0.4.2
## [16] vipor_0.4.7
## [17] vctrs_0.6.5
## [18] utf8_1.2.4
## [19] urlchecker_1.0.1
## [20] units_0.8-5
## [21] tzdb_0.4.0
## [22] tinytex_0.53
## [23] tidyselect_1.2.1
## [24] tidyr_1.3.1
## [25] tibble_3.2.1
## [26] textshaping_0.4.0
## [27] testthat_3.2.1.1
## [28] systemfonts_1.1.0
## [29] sys_3.4.3
## [30] stringi_1.8.4
## [31] statmod_1.5.0
## [32] speedglm_0.3-5
## [33] spdep_1.3-6
## [34] spatstat.utils_3.1-0
## [35] spatstat.sparse_3.1-0
## [36] tensor_1.5
## [37] spatstat.explore_3.3-3
## [38] spatstat.random_3.3-2
## [39] spatstat.geom_3.3-3
## [40] spatstat.univar_3.0-1
## [41] spatstat.data_3.1-2
## [42] spatial_7.3-17
## [43] spam_2.11-0
## [44] spData_2.3.3
## [45] sourcetools_0.1.7-1
## [46] snow_0.4-4
## [47] slider_0.3.2
## [48] slam_0.1-54
## [49] sitmo_2.0.2
## [50] shiny_1.9.1
## [51] shape_1.4.6.1
## [52] sf_1.0-18
## [53] sessioninfo_1.2.2
## [54] seqLogo_1.70.0
## [55] sctransform_0.4.1
## [56] scattermore_1.2
## [57] scales_1.3.0
## [58] sass_0.4.9
## [59] s2_1.1.7
## [60] rversions_2.1.2
## [61] rsvd_1.0.5
## [62] rstudioapi_0.17.1
## [63] rsample_1.2.1
## [64] rprojroot_2.0.4
## [65] rpart_4.1.23
## [66] roxygen2_7.3.2
## [67] rmarkdown_2.28
## [68] rlang_1.1.4
## [69] rjson_0.2.23
## [70] rhdf5filters_1.16.0
## [71] reticulate_1.39.0
## [72] restfulr_0.0.15
## [73] reshape2_1.4.4
## [74] renv_1.0.11.9000
## [75] remotes_2.5.0
## [76] rematch2_2.1.2
## [77] readr_2.1.5
## [78] rcmdcheck_1.4.0
## [79] rappdirs_0.3.3
## [80] ragg_1.3.3
## [81] pwalign_1.0.0
## [82] purrr_1.0.2
## [83] pscl_1.5.9
## [84] ps_1.8.1
## [85] proxy_0.4-27
## [86] promises_1.3.0
## [87] progressr_0.15.0
## [88] progress_1.2.3
## [89] profvis_0.4.0
## [90] processx_3.8.4
## [91] prettyunits_1.2.0
## [92] praise_1.0.0
## [93] pracma_2.4.4
## [94] poweRlaw_0.80.0
## [95] polyclip_1.10-7
## [96] png_0.1-8
## [97] plotly_4.10.4
## [98] plogr_0.2.0
## [99] pkgload_1.4.0
## [100] pkgdown_2.1.1
## [101] pkgconfig_2.0.3
## [102] pkgbuild_1.4.5
## [103] pillar_1.9.0
## [104] pbmcapply_1.5.1
## [105] pbapply_1.7-2
## [106] patchwork_1.3.0
## [107] parallelly_1.38.0
## [108] openssl_2.2.2
## [109] nnet_7.3-19
## [110] nloptr_2.1.1
## [111] munsell_0.5.1
## [112] minqa_1.2.8
## [113] miniUI_0.1.1.1
## [114] mime_0.12
## [115] mgcv_1.9-1
## [116] nlme_3.1-166
## [117] metapod_1.12.0
## [118] memoise_2.0.1
## [119] locfit_1.5-9.10
## [120] lmtest_0.9-40
## [121] zoo_1.8-12
## [122] lme4_1.1-35.5
## [123] listenv_0.9.1
## [124] lifecycle_1.0.4
## [125] leidenbase_0.1.31
## [126] leiden_0.4.3.1
## [127] lazyeval_0.2.2
## [128] lattice_0.22-6
## [129] later_1.3.2
## [130] lambda.r_1.2.4
## [131] labeling_0.4.3
## [132] knitr_1.48
## [133] jsonlite_1.8.9
## [134] jquerylib_0.1.4
## [135] isoband_0.2.7
## [136] irlba_2.3.5.1
## [137] ini_0.3.1
## [138] ica_1.0-3
## [139] httr2_1.0.5
## [140] httr_1.4.7
## [141] httpuv_1.6.15
## [142] htmlwidgets_1.6.4
## [143] htmltools_0.5.8.1
## [144] hms_1.1.3
## [145] highr_0.11
## [146] here_1.0.1
## [147] grr_0.9.5
## [148] gplots_3.2.0
## [149] goftest_1.2-3
## [150] glue_1.8.0
## [151] globals_0.16.3
## [152] gitcreds_0.1.2
## [153] gh_1.4.1
## [154] ggrastr_1.0.2
## [155] ggbeeswarm_0.7.2
## [156] gert_2.1.4
## [157] generics_0.1.3
## [158] future.apply_1.11.3
## [159] futile.options_1.0.1
## [160] futile.logger_1.4.3
## [161] furrr_0.3.1
## [162] future_1.34.0
## [163] fs_1.6.4
## [164] formatR_1.14
## [165] foreign_0.8-86
## [166] fontawesome_0.5.2
## [167] fitdistrplus_1.2-1
## [168] survival_3.7-0
## [169] fastmap_1.2.0
## [170] fastDummies_1.7.4
## [171] farver_2.1.2
## [172] fansi_1.0.6
## [173] evaluate_1.0.1
## [174] ellipsis_0.3.2
## [175] edgeR_4.2.2
## [176] limma_3.60.6
## [177] e1071_1.7-16
## [178] dqrng_0.4.1
## [179] dplyr_1.1.4
## [180] downlit_0.4.4
## [181] dotCall64_1.2
## [182] doParallel_1.0.17
## [183] iterators_1.0.14
## [184] foreach_1.5.2
## [185] digest_0.6.37
## [186] diffobj_0.3.5
## [187] desc_1.4.3
## [188] deldir_2.0-4
## [189] curl_5.2.3
## [190] crosstalk_1.2.1
## [191] credentials_2.0.2
## [192] crayon_1.5.3
## [193] cpp11_0.5.0
## [194] cowplot_1.1.3
## [195] commonmark_1.9.2
## [196] colorspace_2.1-1
## [197] codetools_0.2-20
## [198] cluster_2.1.6
## [199] clue_0.3-65
## [200] clipr_0.8.0
## [201] cli_3.6.3
## [202] classInt_0.4-10
## [203] class_7.3-22
## [204] callr_3.7.6
## [205] cachem_1.1.0
## [206] caTools_1.18.3
## [207] bslib_0.8.0
## [208] brio_1.1.5
## [209] brew_1.0-10
## [210] boot_1.3-30
## [211] bluster_1.14.0
## [212] blob_1.2.4
## [213] bitops_1.0-9
## [214] bit64_4.5.2
## [215] bit_4.5.0
## [216] biglm_0.9-3
## [217] beeswarm_0.4.0
## [218] beachmat_2.20.0
## [219] batchelor_1.20.0
## [220] base64enc_0.1-3
## [221] assertthat_0.2.1
## [222] askpass_1.2.1
## [223] annotate_1.82.0
## [224] XML_3.99-0.17
## [225] UCSC.utils_1.0.0
## [226] TFMPvalue_0.0.9
## [227] TFBSTools_1.42.0
## [228] ScaledMatrix_1.12.0
## [229] Rhtslib_3.0.0
## [230] RhpcBLASctl_0.23-42
## [231] Rhdf5lib_1.26.0
## [232] ResidualMatrix_1.14.1
## [233] RcppTOML_0.2.2
## [234] RcppProgress_0.4.2
## [235] RcppHNSW_0.6.0
## [236] RcppEigen_0.3.4.0.2
## [237] RcppAnnoy_0.0.22
## [238] RSpectra_0.16-2
## [239] RSQLite_2.3.7
## [240] ROCR_1.0-11
## [241] RCurl_1.98-1.16
## [242] RColorBrewer_1.1-3
## [243] RANN_2.6.2
## [244] R6_2.5.1
## [245] R.utils_2.12.3
## [246] R.oo_1.26.0
## [247] R.methodsS3_1.8.2
## [248] MASS_7.3-61
## [249] KernSmooth_2.23-24
## [250] KEGGREST_1.44.1
## [251] HDF5Array_1.32.1
## [252] GlobalOptions_0.1.2
## [253] GetoptLong_1.0.5
## [254] GenomicAlignments_1.40.0
## [255] Rsamtools_2.20.0
## [256] GenomeInfoDbData_1.2.12
## [257] GO.db_3.19.1
## [258] FNN_1.1.4.1
## [259] DirichletMultinomial_1.46.0
## [260] DelayedMatrixStats_1.26.0
## [261] DelayedArray_0.30.1
## [262] SparseArray_1.4.8
## [263] S4Arrays_1.4.1
## [264] abind_1.4-8
## [265] DT_0.33
## [266] DBI_1.2.3
## [267] Cairo_1.6-2
## [268] CNEr_1.40.0
## [269] BiocVersion_3.19.1
## [270] BiocSingular_1.20.0
## [271] BiocParallel_1.38.0
## [272] BiocNeighbors_1.22.0
## [273] BiocManager_1.30.25
## [274] BH_1.84.0-0
## [275] EnsDb.Hsapiens.v86_2.99.0
## [276] ensembldb_2.28.1
## [277] AnnotationFilter_1.28.0
## [278] BSgenome.Hsapiens.UCSC.hg38_1.4.5
## [279] slingshot_2.12.0
## [280] TrajectoryUtils_1.12.0
## [281] princurve_2.1.6
## [282] monocle3_1.3.7
## [283] chromVAR_1.26.0
## [284] ggseqlogo_0.2
## [285] chromVARmotifs_0.2.0
## [286] motifmatchr_1.26.0
## [287] presto_1.0.0
## [288] ggrepel_0.9.6
## [289] hexbin_1.28.4
## [290] circlize_0.4.16
## [291] ComplexHeatmap_2.20.0
## [292] Rtsne_0.17
## [293] igraph_2.1.1
## [294] scran_1.32.0
## [295] scuttle_1.14.0
## [296] SingleCellExperiment_1.26.0
## [297] pheatmap_1.0.12
## [298] harmony_1.2.1
## [299] uwot_0.2.2
## [300] ggridges_0.5.6
## [301] BSgenome.Hsapiens.UCSC.hg19_1.4.3
## [302] nabor_0.5.0
## [303] Seurat_5.1.0
## [304] SeuratObject_5.0.2
## [305] sp_2.1-4
## [306] pdftools_3.4.1
## [307] org.Dm.eg.db_3.19.1
## [308] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0
## [309] GenomicFeatures_1.56.0
## [310] AnnotationDbi_1.66.0
## [311] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1
## [312] BSgenome_1.72.0
## [313] rtracklayer_1.64.0
## [314] BiocIO_1.14.0
## [315] Biostrings_2.72.1
## [316] XVector_0.44.0
## [317] rhdf5_2.48.0
## [318] SummarizedExperiment_1.34.0
## [319] Biobase_2.64.0
## [320] RcppArmadillo_14.0.2-1
## [321] Rcpp_1.0.13
## [322] Matrix_1.7-1
## [323] GenomicRanges_1.56.2
## [324] GenomeInfoDb_1.40.1
## [325] IRanges_2.38.1
## [326] S4Vectors_0.42.1
## [327] BiocGenerics_0.50.0
## [328] sparseMatrixStats_1.16.0
## [329] MatrixGenerics_1.16.0
## [330] matrixStats_1.4.1
## [331] data.table_1.16.2
## [332] stringr_1.5.1
## [333] plyr_1.8.9
## [334] magrittr_2.0.3
## [335] ggplot2_3.5.1
## [336] gtable_0.3.6
## [337] gtools_3.9.5
## [338] gridExtra_2.3
## [339] devtools_2.4.5
## [340] usethis_3.0.0
## [341] ArchR_1.0.3
##
## loaded via a namespace (and not attached):
## [1] ProtGenerics_1.36.0 tools_4.4.1 bookdown_0.41
## [4] qpdf_1.3.4 splines_4.4.1 compiler_4.4.1
## [7] svglite_2.1.3