Chapter 4 Contact and Session Information
4.1 Contact information
For any queries, contact Alysha De Livera (a.delivera@latrobe.edu.au) or Agus Salim (salim.a@unimelb.edu.au).
4.2 Session information
sessionInfo()## R version 4.2.1 (2022-06-23 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19044)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_Australia.utf8
## [2] LC_CTYPE=English_Australia.utf8
## [3] LC_MONETARY=English_Australia.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_Australia.utf8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils
## [6] datasets methods base
##
## other attached packages:
## [1] HDF5Array_1.26.0 rhdf5_2.42.0
## [3] DelayedArray_0.24.0 igraph_1.3.5
## [5] gridExtra_2.3 pheatmap_1.0.12
## [7] dittoSeq_1.10.0 randomcoloR_1.1.0.1
## [9] SeuratObject_4.1.3 Seurat_4.3.0
## [11] scMerge_1.14.0 uwot_0.1.14
## [13] Matrix_1.5-3 forcats_0.5.2
## [15] stringr_1.5.0 dplyr_1.0.10
## [17] purrr_0.3.5 readr_2.1.3
## [19] tidyr_1.2.1 tibble_3.1.8
## [21] tidyverse_1.3.2 hrbrthemes_0.8.0
## [23] celldex_1.8.0 SingleR_2.0.0
## [25] edgeR_3.40.0 limma_3.54.0
## [27] scran_1.26.0 scater_1.26.1
## [29] scuttle_1.8.1 SingleCellExperiment_1.20.0
## [31] SummarizedExperiment_1.28.0 Biobase_2.58.0
## [33] GenomicRanges_1.50.1 GenomeInfoDb_1.34.4
## [35] IRanges_2.32.0 S4Vectors_0.36.0
## [37] BiocGenerics_0.44.0 MatrixGenerics_1.10.0
## [39] matrixStats_0.63.0 ruvIIInb_0.7.8.5
## [41] showtext_0.9-5 showtextdb_3.0
## [43] sysfonts_0.8.8 ggplot2_3.4.0
## [45] extrafont_0.18
##
## loaded via a namespace (and not attached):
## [1] rsvd_1.0.5
## [2] Hmisc_4.7-2
## [3] ica_1.0-3
## [4] ps_1.7.2
## [5] lmtest_0.9-40
## [6] crayon_1.5.2
## [7] V8_4.2.2
## [8] rhdf5filters_1.10.0
## [9] MASS_7.3-58.1
## [10] nlme_3.1-160
## [11] backports_1.4.1
## [12] reprex_2.0.2
## [13] rlang_1.0.6
## [14] XVector_0.38.0
## [15] ROCR_1.0-11
## [16] readxl_1.4.1
## [17] irlba_2.3.5.1
## [18] extrafontdb_1.0
## [19] callr_3.7.3
## [20] filelock_1.0.2
## [21] BiocParallel_1.32.4
## [22] bit64_4.0.5
## [23] glue_1.6.2
## [24] loo_2.5.1
## [25] sctransform_0.3.5
## [26] sfsmisc_1.1-14
## [27] rstan_2.21.7
## [28] parallel_4.2.1
## [29] processx_3.8.0
## [30] vipor_0.4.5
## [31] spatstat.sparse_3.0-0
## [32] AnnotationDbi_1.60.0
## [33] spatstat.geom_3.0-3
## [34] haven_2.5.1
## [35] tidyselect_1.2.0
## [36] fitdistrplus_1.1-8
## [37] zoo_1.8-11
## [38] distr_2.9.1
## [39] xtable_1.8-4
## [40] magrittr_2.0.3
## [41] evaluate_0.18
## [42] gdtools_0.2.4
## [43] cli_3.4.1
## [44] zlibbioc_1.44.0
## [45] rstudioapi_0.14
## [46] miniUI_0.1.1.1
## [47] sp_1.5-1
## [48] bslib_0.4.1
## [49] rpart_4.1.19
## [50] shiny_1.7.3
## [51] BiocSingular_1.14.0
## [52] xfun_0.35
## [53] inline_0.3.19
## [54] pkgbuild_1.4.0
## [55] cluster_2.1.4
## [56] caTools_1.18.2
## [57] KEGGREST_1.38.0
## [58] interactiveDisplayBase_1.36.0
## [59] ggrepel_0.9.2
## [60] listenv_0.8.0
## [61] Biostrings_2.66.0
## [62] png_0.1-8
## [63] future_1.29.0
## [64] withr_2.5.0
## [65] bitops_1.0-7
## [66] plyr_1.8.8
## [67] cellranger_1.1.0
## [68] dqrng_0.3.0
## [69] pillar_1.8.1
## [70] RcppParallel_5.1.5
## [71] gplots_3.1.3
## [72] cachem_1.0.6
## [73] reldist_1.7-1
## [74] fs_1.5.2
## [75] DelayedMatrixStats_1.20.0
## [76] vctrs_0.5.1
## [77] ellipsis_0.3.2
## [78] generics_0.1.3
## [79] tools_4.2.1
## [80] foreign_0.8-83
## [81] beeswarm_0.4.0
## [82] munsell_0.5.0
## [83] proxy_0.4-27
## [84] fastmap_1.1.0
## [85] compiler_4.2.1
## [86] abind_1.4-5
## [87] httpuv_1.6.6
## [88] ExperimentHub_2.6.0
## [89] densEstBayes_1.0-2.1
## [90] plotly_4.10.1
## [91] GenomeInfoDbData_1.2.9
## [92] lattice_0.20-45
## [93] deldir_1.0-6
## [94] utf8_1.2.2
## [95] M3Drop_1.24.0
## [96] later_1.3.0
## [97] BiocFileCache_2.6.0
## [98] jsonlite_1.8.3
## [99] scales_1.2.1
## [100] ScaledMatrix_1.6.0
## [101] pbapply_1.6-0
## [102] sparseMatrixStats_1.10.0
## [103] lazyeval_0.2.2
## [104] promises_1.2.0.1
## [105] latticeExtra_0.6-30
## [106] goftest_1.2-3
## [107] spatstat.utils_3.0-1
## [108] reticulate_1.26
## [109] checkmate_2.1.0
## [110] rmarkdown_2.18
## [111] cowplot_1.1.1
## [112] statmod_1.4.37
## [113] Rtsne_0.16
## [114] survival_3.4-0
## [115] numDeriv_2016.8-1.1
## [116] rsconnect_0.8.28
## [117] yaml_2.3.6
## [118] systemfonts_1.0.4
## [119] htmltools_0.5.3
## [120] memoise_2.0.1
## [121] locfit_1.5-9.6
## [122] viridisLite_0.4.1
## [123] digest_0.6.29
## [124] assertthat_0.2.1
## [125] mime_0.12
## [126] rappdirs_0.3.3
## [127] Rttf2pt1_1.3.11
## [128] RSQLite_2.2.19
## [129] future.apply_1.10.0
## [130] data.table_1.14.6
## [131] blob_1.2.3
## [132] splines_4.2.1
## [133] Formula_1.2-4
## [134] labeling_0.4.2
## [135] Rhdf5lib_1.20.0
## [136] googledrive_2.0.0
## [137] AnnotationHub_3.6.0
## [138] RCurl_1.98-1.9
## [139] broom_1.0.1
## [140] hms_1.1.2
## [141] modelr_0.1.10
## [142] colorspace_2.0-3
## [143] base64enc_0.1-3
## [144] BiocManager_1.30.19
## [145] ggbeeswarm_0.6.0
## [146] nnet_7.3-18
## [147] sass_0.4.4
## [148] Rcpp_1.0.9
## [149] bookdown_0.30
## [150] RANN_2.6.1
## [151] mvtnorm_1.1-3
## [152] fansi_1.0.3
## [153] tzdb_0.3.0
## [154] parallelly_1.32.1
## [155] R6_2.5.1
## [156] grid_4.2.1
## [157] ggridges_0.5.4
## [158] lifecycle_1.0.3
## [159] StanHeaders_2.21.0-7
## [160] bluster_1.8.0
## [161] curl_4.3.3
## [162] googlesheets4_1.0.1
## [163] leiden_0.4.3
## [164] jquerylib_0.1.4
## [165] RcppAnnoy_0.0.20
## [166] RColorBrewer_1.1-3
## [167] spatstat.explore_3.0-5
## [168] htmlwidgets_1.5.4
## [169] beachmat_2.14.0
## [170] polyclip_1.10-4
## [171] timechange_0.1.1
## [172] rvest_1.0.3
## [173] mgcv_1.8-41
## [174] globals_0.16.2
## [175] htmlTable_2.4.1
## [176] patchwork_1.1.2
## [177] spatstat.random_3.0-1
## [178] bdsmatrix_1.3-6
## [179] progressr_0.11.0
## [180] codetools_0.2-18
## [181] lubridate_1.9.0
## [182] metapod_1.6.0
## [183] gtools_3.9.4
## [184] prettyunits_1.1.1
## [185] dbplyr_2.2.1
## [186] gtable_0.3.1
## [187] DBI_1.1.3
## [188] tensor_1.5
## [189] httr_1.4.4
## [190] highr_0.9
## [191] KernSmooth_2.23-20
## [192] stringi_1.7.8
## [193] reshape2_1.4.4
## [194] farver_2.1.1
## [195] viridis_0.6.2
## [196] xml2_1.3.3
## [197] bbmle_1.0.25
## [198] BiocNeighbors_1.16.0
## [199] interp_1.1-3
## [200] scattermore_0.8
## [201] BiocVersion_3.16.0
## [202] bit_4.0.5
## [203] jpeg_0.1-10
## [204] spatstat.data_3.0-0
## [205] pkgconfig_2.0.3
## [206] gargle_1.2.1
## [207] ruv_0.9.7.1
## [208] knitr_1.41
## [209] startupmsg_0.9.6