Chapter 24 Session Information
This tutorial was run on the date specified below.
## [1] "2022-12-23"The sessionInfo() at run time was:
sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Rocky Linux 8.5 (Green Obsidian)
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so
##
## 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
##
## attached base packages:
## [1] compiler parallel stats4 grid stats graphics grDevices
## [8] datasets utils methods base
##
## other attached packages:
## [1] zlibbioc_1.40.0
## [2] zip_2.2.0
## [3] yaml_2.2.1
## [4] xtable_1.8-4
## [5] xopen_1.0.0
## [6] xml2_1.3.3
## [7] xfun_0.35
## [8] withr_2.4.3
## [9] whisker_0.4
## [10] waldo_0.3.1
## [11] vroom_1.5.6
## [12] viridisLite_0.4.0
## [13] vctrs_0.5.1
## [14] utf8_1.2.2
## [15] tzdb_0.2.0
## [16] tidyselect_1.1.1
## [17] tidyr_1.1.4
## [18] tibble_3.1.6
## [19] testthat_3.1.1
## [20] sys_3.4
## [21] stringi_1.7.6
## [22] statmod_1.4.36
## [23] spatstat.utils_2.2-0
## [24] spatstat.sparse_2.0-0
## [25] tensor_1.5
## [26] spatstat.core_2.3-1
## [27] spatstat.geom_2.3-0
## [28] spatstat.data_2.1-0
## [29] spatial_7.3-14
## [30] sourcetools_0.1.7
## [31] snow_0.4-4
## [32] sitmo_2.0.2
## [33] shinythemes_1.2.0
## [34] shiny_1.7.1
## [35] shape_1.4.6
## [36] sessioninfo_1.2.1
## [37] seqLogo_1.60.0
## [38] sctransform_0.3.2
## [39] scattermore_0.7
## [40] scales_1.1.1
## [41] sass_0.4.0
## [42] rversions_2.1.1
## [43] rsvd_1.0.5
## [44] rstudioapi_0.13
## [45] rprojroot_2.0.2
## [46] rpart_4.1-15
## [47] roxygen2_7.1.2
## [48] rlang_1.0.6
## [49] rjson_0.2.21
## [50] rhdf5filters_1.6.0
## [51] rhandsontable_0.3.8
## [52] reticulate_1.22
## [53] restfulr_0.0.13
## [54] reshape2_1.4.4
## [55] renv_0.16.0
## [56] remotes_2.4.2
## [57] rematch2_2.1.2
## [58] readr_2.1.0
## [59] rcmdcheck_1.4.0
## [60] rappdirs_0.3.3
## [61] purrr_0.3.4
## [62] ps_1.6.0
## [63] promises_1.2.0.1
## [64] progress_1.2.2
## [65] processx_3.8.0
## [66] prettyunits_1.1.1
## [67] praise_1.0.0
## [68] pracma_2.3.3
## [69] poweRlaw_0.70.6
## [70] polyclip_1.10-0
## [71] png_0.1-7
## [72] plotly_4.10.0
## [73] plogr_0.2.0
## [74] pkgload_1.2.4
## [75] pkgconfig_2.0.3
## [76] pkgbuild_1.2.1
## [77] pillar_1.6.4
## [78] pbapply_1.5-0
## [79] patchwork_1.1.1
## [80] parallelly_1.28.1
## [81] openssl_1.4.5
## [82] nnet_7.3-16
## [83] munsell_0.5.0
## [84] miniUI_0.1.1.1
## [85] mime_0.12
## [86] mgcv_1.8-38
## [87] nlme_3.1-153
## [88] metapod_1.2.0
## [89] memoise_2.0.1
## [90] locfit_1.5-9.4
## [91] lmtest_0.9-39
## [92] zoo_1.8-9
## [93] listenv_0.8.0
## [94] lifecycle_1.0.3
## [95] leiden_0.3.9
## [96] lazyeval_0.2.2
## [97] later_1.3.0
## [98] lambda.r_1.2.4
## [99] labeling_0.4.2
## [100] knitr_1.41
## [101] jsonlite_1.7.2
## [102] jquerylib_0.1.4
## [103] isoband_0.2.5
## [104] irlba_2.3.3
## [105] ini_0.3.1
## [106] ica_1.0-2
## [107] httr_1.4.2
## [108] httpuv_1.6.3
## [109] htmlwidgets_1.5.4
## [110] htmltools_0.5.2
## [111] hms_1.1.1
## [112] highr_0.9
## [113] here_1.0.1
## [114] gplots_3.1.1
## [115] goftest_1.2-3
## [116] glue_1.5.1
## [117] globals_0.14.0
## [118] gitcreds_0.1.1
## [119] gh_1.3.0
## [120] gert_1.4.3
## [121] generics_0.1.1
## [122] geneplotter_1.72.0
## [123] lattice_0.20-45
## [124] genefilter_1.76.0
## [125] future.apply_1.8.1
## [126] future_1.23.0
## [127] futile.options_1.0.1
## [128] futile.logger_1.4.3
## [129] fs_1.5.0
## [130] formatR_1.11
## [131] foreign_0.8-81
## [132] fontawesome_0.2.2
## [133] fitdistrplus_1.1-6
## [134] survival_3.2-13
## [135] fastmap_1.1.0
## [136] farver_2.1.0
## [137] fansi_0.5.0
## [138] evaluate_0.19
## [139] ellipsis_0.3.2
## [140] edgeR_3.36.0
## [141] limma_3.50.0
## [142] dqrng_0.3.0
## [143] dplyr_1.0.10
## [144] doParallel_1.0.16
## [145] iterators_1.0.13
## [146] foreach_1.5.1
## [147] digest_0.6.29
## [148] diffobj_0.3.5
## [149] desc_1.4.0
## [150] deldir_1.0-6
## [151] curl_4.3.2
## [152] crosstalk_1.2.0
## [153] credentials_1.3.2
## [154] crayon_1.4.2
## [155] cpp11_0.4.2
## [156] cowplot_1.1.1
## [157] commonmark_1.7
## [158] colorspace_2.0-2
## [159] codetools_0.2-18
## [160] cluster_2.1.2
## [161] clue_0.3-60
## [162] clipr_0.7.1
## [163] cli_3.5.0
## [164] class_7.3-19
## [165] callr_3.7.3
## [166] cachem_1.0.6
## [167] caTools_1.18.2
## [168] bslib_0.3.1
## [169] brio_1.1.3
## [170] brew_1.0-6
## [171] boot_1.3-28
## [172] bluster_1.4.0
## [173] blob_1.2.2
## [174] bitops_1.0-7
## [175] bit64_4.0.5
## [176] bit_4.0.4
## [177] beachmat_2.10.0
## [178] base64enc_0.1-3
## [179] askpass_1.1
## [180] annotate_1.72.0
## [181] abind_1.4-5
## [182] XML_3.99-0.8
## [183] TFMPvalue_0.0.8
## [184] TFBSTools_1.32.0
## [185] ScaledMatrix_1.2.0
## [186] Rhtslib_1.26.0
## [187] Rhdf5lib_1.16.0
## [188] RcppProgress_0.4.2
## [189] RcppHNSW_0.3.0
## [190] RcppEigen_0.3.3.9.1
## [191] RcppAnnoy_0.0.19
## [192] RSpectra_0.16-0
## [193] RSQLite_2.2.8
## [194] ROCR_1.0-11
## [195] RCurl_1.98-1.5
## [196] RColorBrewer_1.1-2
## [197] RANN_2.6.1
## [198] R6_2.5.1
## [199] R.utils_2.11.0
## [200] R.oo_1.24.0
## [201] R.methodsS3_1.8.1
## [202] MASS_7.3-54
## [203] KernSmooth_2.23-20
## [204] KEGGREST_1.34.0
## [205] GlobalOptions_0.1.2
## [206] GetoptLong_1.0.5
## [207] GenomicAlignments_1.30.0
## [208] Rsamtools_2.10.0
## [209] GenomeInfoDbData_1.2.7
## [210] GO.db_3.14.0
## [211] FNN_1.1.3
## [212] DirichletMultinomial_1.36.0
## [213] DelayedMatrixStats_1.16.0
## [214] DelayedArray_0.20.0
## [215] DT_0.20
## [216] DESeq2_1.34.0
## [217] DBI_1.1.1
## [218] Cairo_1.5-12.2
## [219] CNEr_1.30.0
## [220] BiocVersion_3.14.0
## [221] BiocSingular_1.10.0
## [222] BiocParallel_1.28.2
## [223] BiocNeighbors_1.12.0
## [224] BiocManager_1.30.16
## [225] BiocIO_1.4.0
## [226] BH_1.75.0-0
## [227] EnsDb.Hsapiens.v86_2.99.0
## [228] ensembldb_2.18.4
## [229] AnnotationFilter_1.18.0
## [230] BSgenome.Hsapiens.UCSC.hg38_1.4.4
## [231] slingshot_2.2.1
## [232] TrajectoryUtils_1.2.0
## [233] princurve_2.1.6
## [234] monocle3_1.3.1
## [235] chromVAR_1.16.0
## [236] ggseqlogo_0.1
## [237] chromVARmotifs_0.2.0
## [238] motifmatchr_1.16.0
## [239] presto_1.0.0
## [240] ggrepel_0.9.1
## [241] hexbin_1.28.2
## [242] circlize_0.4.13
## [243] ComplexHeatmap_2.10.0
## [244] Rtsne_0.15
## [245] igraph_1.3.5
## [246] scran_1.22.1
## [247] scuttle_1.4.0
## [248] SingleCellExperiment_1.16.0
## [249] pheatmap_1.0.12
## [250] harmony_0.1.1
## [251] uwot_0.1.10
## [252] ggridges_0.5.3
## [253] BSgenome.Hsapiens.UCSC.hg19_1.4.3
## [254] nabor_0.5.0
## [255] SeuratObject_4.0.3
## [256] Seurat_4.0.5
## [257] pdftools_3.3.2
## [258] org.Dm.eg.db_3.14.0
## [259] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0
## [260] GenomicFeatures_1.46.5
## [261] AnnotationDbi_1.56.2
## [262] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1
## [263] BSgenome_1.62.0
## [264] rtracklayer_1.54.0
## [265] Biostrings_2.62.0
## [266] XVector_0.34.0
## [267] rhdf5_2.38.0
## [268] SummarizedExperiment_1.24.0
## [269] Biobase_2.54.0
## [270] RcppArmadillo_0.10.7.3.0
## [271] Rcpp_1.0.7
## [272] Matrix_1.3-4
## [273] GenomicRanges_1.46.1
## [274] GenomeInfoDb_1.30.0
## [275] IRanges_2.28.0
## [276] S4Vectors_0.32.4
## [277] BiocGenerics_0.40.0
## [278] sparseMatrixStats_1.6.0
## [279] MatrixGenerics_1.6.0
## [280] matrixStats_0.61.0
## [281] data.table_1.14.2
## [282] stringr_1.4.0
## [283] plyr_1.8.6
## [284] magrittr_2.0.1
## [285] ggplot2_3.3.5
## [286] gtable_0.3.0
## [287] gtools_3.9.2
## [288] gridExtra_2.3
## [289] devtools_2.4.3
## [290] usethis_2.1.3
## [291] ArchR_1.0.3
##
## loaded via a namespace (and not attached):
## [1] terra_1.6-47 nloptr_2.0.3 bookdown_0.31
## [4] ggbeeswarm_0.7.1 minqa_1.2.5 beeswarm_0.4.0
## [7] systemfonts_1.0.4 leidenbase_0.1.14 dbplyr_2.2.1
## [10] vipor_0.4.5 qpdf_1.3.0 BiocFileCache_2.2.1
## [13] ProtGenerics_1.26.0 tools_4.1.1 proxy_0.4-27
## [16] assertthat_0.2.1 rmarkdown_2.19 ggrastr_1.0.1
## [19] splines_4.1.1 biomaRt_2.50.3 filelock_1.0.2
## [22] lme4_1.1-31 viridis_0.6.2 svglite_2.1.0