Record the technical metadata for the for a Seurat object
record_experiment_data(
object,
experiment_name = "default_experiment",
organism = "human"
)A seurat objet
Name of the experiment
Organism
logged_seu <- record_experiment_data(human_gene_transcript_seu, experiment_name = "human_gene_transcript", organism = "mouse")
#> [13:35:22] Logging Technical Details...
Misc(logged_seu, "experiment")
#> $experiment_name
#> [1] "default_experiment"
#>
#> $organism
#> Homo_sapiens
#> "human"
#>
#> $date_of_export
#> [1] "2024-06-14"
#>
#> $date_of_analysis
#> [1] "2024-06-14"
#>
#> $parameters
#> $parameters$gene_nomenclature
#> [1] "gene_symbol"
#>
#> $parameters$discard_genes_expressed_in_fewer_cells_than
#> [1] 10
#>
#> $parameters$keep_mitochondrial_genes
#> [1] TRUE
#>
#> $parameters$variables_to_regress_out
#> [1] "nCount_RNA"
#>
#> $parameters$number_PCs
#> [1] 30
#>
#> $parameters$tSNE_perplexity
#> [1] 30
#>
#> $parameters$cluster_resolution
#> [1] 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0
#>
#>
#> $filtering
#> $filtering$UMI_min
#> [1] 50
#>
#> $filtering$genes_min
#> [1] 10
#>
#>
#> $session_info
#> $session_info[[1]]
#> [1] "\033[1m\033[36m─ Session info ───────────────────────────────────────────────────────────────\033[39m\033[22m"
#> [2] " \033[3m\033[90msetting \033[39m\033[23m \033[3m\033[90mvalue\033[39m\033[23m"
#> [3] " version R Under development (unstable) (2024-01-29 r85841)"
#> [4] " os Ubuntu 20.04.4 LTS"
#> [5] " system x86_64, linux-gnu"
#> [6] " ui X11"
#> [7] " language en"
#> [8] " collate C"
#> [9] " ctype en_US.UTF-8"
#> [10] " tz America/Los_Angeles"
#> [11] " date 2024-06-14"
#> [12] " pandoc 3.1.12.1 @ /dataVolume/miniconda3/envs/scvelo/bin/ (via rmarkdown)"
#> [13] ""
#> [14] "\033[1m\033[36m─ Packages ───────────────────────────────────────────────────────────────────\033[39m\033[22m"
#> [15] " \033[3m\033[90mpackage \033[39m\033[23m \033[3m\033[90m*\033[39m\033[23m \033[3m\033[90mversion \033[39m\033[23m \033[3m\033[90mdate (UTC)\033[39m\033[23m \033[3m\033[90mlib\033[39m\033[23m \033[3m\033[90msource\033[39m\033[23m"
#> [16] " abind 1.4-5 \033[90m2016-07-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [17] " annotables 0.2.0 \033[90m2023-11-07\033[39m \033[90m[2]\033[39m \033[1m\033[35mGithub (stephenturner/annotables@d2e86c7)\033[39m\033[22m"
#> [18] " AnnotationDbi 1.65.2 \033[90m2023-11-03\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [19] " AnnotationFilter 1.27.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [20] " AnnotationHub * 3.11.1 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [21] " assertthat 0.2.1 \033[90m2019-03-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [22] " backports 1.4.1 \033[90m2021-12-13\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [23] " basilisk 1.15.4 \033[90m2024-01-29\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [24] " basilisk.utils 1.15.1 \033[90m2023-11-19\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [25] " beachmat 2.19.1 \033[90m2024-01-22\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [26] " beeswarm 0.4.0 \033[90m2021-06-01\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [27] " Biobase * 2.63.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [28] " BiocFileCache * 2.11.1 \033[90m2023-10-26\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [29] " BiocGenerics * 0.49.1 \033[90m2023-11-01\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [30] " BiocIO 1.13.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [31] " BiocManager 1.30.22 \033[90m2023-08-08\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [32] " BiocNeighbors 1.21.2 \033[90m2023-12-19\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [33] " BiocParallel 1.37.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [34] " BiocSingular 1.19.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [35] " BiocVersion 3.19.1 \033[90m2023-10-26\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [36] " biomaRt 2.59.1 \033[90m2024-01-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [37] " Biostrings 2.71.2 \033[90m2024-01-28\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [38] " bit 4.0.5 \033[90m2022-11-15\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [39] " bit64 4.0.5 \033[90m2020-08-30\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [40] " bitops 1.0-7 \033[90m2021-04-24\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [41] " blob 1.2.4 \033[90m2023-03-17\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [42] " bluster 1.13.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [43] " boot 1.3-28.1 \033[90m2022-11-22\033[39m \033[90m[3]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [44] " bslib 0.6.1 \033[90m2023-11-28\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [45] " cachem 1.0.8 \033[90m2023-05-01\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [46] " checkmate 2.3.1 \033[90m2023-12-04\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [47] " chevreuldata * 0.99.0 \033[90m2024-03-29\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [48] " cli 3.6.2 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [49] " cluster 2.1.6 \033[90m2023-12-01\033[39m \033[90m[3]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [50] " codetools 0.2-19 \033[90m2023-02-01\033[39m \033[90m[3]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [51] " colorspace 2.1-0 \033[90m2023-01-23\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [52] " cowplot 1.1.3 \033[90m2024-01-22\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [53] " crayon 1.5.2 \033[90m2022-09-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [54] " curl 5.2.0 \033[90m2023-12-08\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [55] " data.table 1.15.0 \033[90m2024-01-30\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [56] " DataEditR 0.1.6 \033[90m2023-11-07\033[39m \033[90m[2]\033[39m \033[1m\033[35mGithub (DillonHammill/DataEditR@850feb2)\033[39m\033[22m"
#> [57] " DBI 1.2.2 \033[90m2024-02-16\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [58] " dbplyr * 2.4.0 \033[90m2023-10-26\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [59] " DelayedArray 0.29.5 \033[90m2024-02-23\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [60] " DelayedMatrixStats 1.25.1 \033[90m2023-11-09\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [61] " deldir 2.0-2 \033[90m2023-11-23\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [62] " desc 1.4.3 \033[90m2023-12-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [63] " devtools 2.4.5 \033[90m2022-10-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [64] " digest 0.6.34 \033[90m2024-01-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [65] " dir.expiry 1.11.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [66] " dotCall64 1.1-1 \033[90m2023-11-28\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [67] " downlit 0.4.3 \033[90m2023-06-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [68] " dplyr 1.1.4 \033[90m2023-11-17\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [69] " dqrng 0.3.2 \033[90m2023-11-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [70] " edgeR 4.1.15 \033[90m2024-01-29\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [71] " ellipsis 0.3.2 \033[90m2021-04-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [72] " EnsDb.Hsapiens.v86 2.99.0 \033[90m2023-08-28\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [73] " ensembldb 2.27.1 \033[90m2023-11-20\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [74] " evaluate 0.23 \033[90m2023-11-01\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [75] " ExperimentHub * 2.11.1 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [76] " fansi 1.0.6 \033[90m2023-12-08\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [77] " farver 2.1.1 \033[90m2022-07-06\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [78] " fastDummies 1.7.3 \033[90m2023-07-06\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [79] " fastmap 1.1.1 \033[90m2023-02-24\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [80] " filelock 1.0.3 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [81] " fitdistrplus 1.1-11 \033[90m2023-04-25\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [82] " forcats 1.0.0 \033[90m2023-01-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [83] " formattable 0.2.1 \033[90m2021-01-07\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [84] " fs 1.6.3 \033[90m2023-07-20\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [85] " future 1.33.1 \033[90m2023-12-22\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [86] " future.apply 1.11.1 \033[90m2023-12-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [87] " generics 0.1.3 \033[90m2022-07-05\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [88] " GenomeInfoDb * 1.39.9 \033[90m2024-03-13\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [89] " GenomeInfoDbData 1.2.11 \033[90m2024-01-31\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [90] " GenomicAlignments 1.39.4 \033[90m2024-02-15\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [91] " GenomicFeatures 1.55.3 \033[90m2024-01-28\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [92] " GenomicRanges * 1.55.3 \033[90m2024-02-13\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [93] " ggbeeswarm 0.7.2 \033[90m2023-04-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [94] " ggforce 0.4.2 \033[90m2024-02-19\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [95] " ggplot2 3.5.0 \033[90m2024-02-23\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [96] " ggraph 2.1.0 \033[90m2022-10-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [97] " ggrastr 1.0.2 \033[90m2023-06-01\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [98] " ggrepel 0.9.5 \033[90m2024-01-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [99] " ggridges 0.5.6 \033[90m2024-01-23\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [100] " globals 0.16.2 \033[90m2022-11-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [101] " glue 1.7.0 \033[90m2024-01-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [102] " goftest 1.2-3 \033[90m2021-10-07\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [103] " graphlayouts 1.1.0 \033[90m2024-01-19\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [104] " gridExtra 2.3 \033[90m2017-09-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [105] " gtable 0.3.4 \033[90m2023-08-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [106] " HDF5Array 1.31.5 \033[90m2024-02-02\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [107] " hms 1.1.3 \033[90m2023-03-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [108] " htmltools 0.5.7 \033[90m2023-11-03\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [109] " htmlwidgets 1.6.4 \033[90m2023-12-06\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [110] " httpuv 1.6.14 \033[90m2024-01-26\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [111] " httr 1.4.7 \033[90m2023-08-15\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [112] " httr2 1.0.0 \033[90m2023-11-14\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [113] " ica 1.0-3 \033[90m2022-07-08\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [114] " igraph 1.5.1 \033[90m2023-08-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [115] " IRanges * 2.37.1 \033[90m2024-01-19\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [116] " irlba 2.3.5.1 \033[90m2022-10-03\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [117] " jquerylib 0.1.4 \033[90m2021-04-26\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [118] " jsonlite 1.8.8 \033[90m2023-12-04\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [119] " KEGGREST 1.43.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [120] " KernSmooth 2.23-22 \033[90m2023-07-10\033[39m \033[90m[3]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [121] " knitr 1.45 \033[90m2023-10-30\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [122] " ks 1.14.2 \033[90m2024-01-15\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [123] " labeling 0.4.3 \033[90m2023-08-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [124] " later 1.3.2 \033[90m2023-12-06\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [125] " lattice 0.22-5 \033[90m2023-10-24\033[39m \033[90m[3]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [126] " lazyeval 0.2.2 \033[90m2019-03-15\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [127] " leiden 0.4.3.1 \033[90m2023-11-17\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [128] " lifecycle 1.0.4 \033[90m2023-11-07\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [129] " limma 3.59.2 \033[90m2024-02-04\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [130] " listenv 0.9.1 \033[90m2024-01-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [131] " lme4 1.1-35.1 \033[90m2023-11-05\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [132] " lmtest 0.9-40 \033[90m2022-03-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [133] " locfit 1.5-9.8 \033[90m2023-06-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [134] " LoomExperiment 1.21.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [135] " lubridate 1.9.3 \033[90m2023-09-27\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [136] " magrittr 2.0.3 \033[90m2022-03-30\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [137] " MASS 7.3-60.2 \033[90m2024-01-30\033[39m \033[90m[3]\033[39m \033[1m\033[35mlocal\033[39m\033[22m"
#> [138] " Matrix 1.6-5 \033[90m2024-01-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [139] " MatrixGenerics * 1.15.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [140] " matrixStats * 1.2.0 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [141] " mclust 6.1 \033[90m2024-02-23\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [142] " memoise 2.0.1 \033[90m2021-11-26\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [143] " metapod 1.11.1 \033[90m2023-12-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [144] " mime 0.12 \033[90m2021-09-28\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [145] " miniUI 0.1.1.1 \033[90m2018-05-18\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [146] " minqa 1.2.6 \033[90m2023-09-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [147] " monocle3 1.3.4 \033[90m2024-01-22\033[39m \033[90m[2]\033[39m \033[1m\033[35mGithub (cole-trapnell-lab/monocle3@2b17745)\033[39m\033[22m"
#> [148] " munsell 0.5.0 \033[90m2018-06-12\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [149] " mvtnorm 1.2-4 \033[90m2023-11-27\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [150] " Nebulosa 1.13.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [151] " nlme 3.1-164 \033[90m2023-11-27\033[39m \033[90m[3]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [152] " nloptr 2.0.3 \033[90m2022-05-26\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [153] " parallelly 1.37.0 \033[90m2024-02-14\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [154] " patchwork 1.2.0 \033[90m2024-01-08\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [155] " pbapply 1.7-2 \033[90m2023-06-27\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [156] " pillar 1.9.0 \033[90m2023-03-22\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [157] " pkgbuild 1.4.3 \033[90m2023-12-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [158] " pkgconfig 2.0.3 \033[90m2019-09-22\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [159] " pkgdown 2.0.7 \033[90m2022-12-14\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [160] " pkgload 1.3.4 \033[90m2024-01-16\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [161] " plotly 4.10.4 \033[90m2024-01-13\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [162] " plyr 1.8.9 \033[90m2023-10-02\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [163] " png 0.1-8 \033[90m2022-11-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [164] " polyclip 1.10-6 \033[90m2023-09-27\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [165] " pracma 2.4.4 \033[90m2023-11-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [166] " presto 1.0.0 \033[90m2023-08-28\033[39m \033[90m[2]\033[39m \033[1m\033[35mGithub (immunogenomics/presto@31dc97f)\033[39m\033[22m"
#> [167] " prettyunits 1.2.0 \033[90m2023-09-24\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [168] " profvis 0.3.8 \033[90m2023-05-02\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [169] " progress 1.2.3 \033[90m2023-12-06\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [170] " progressr 0.14.0 \033[90m2023-08-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [171] " promises 1.2.1 \033[90m2023-08-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [172] " ProtGenerics 1.35.2 \033[90m2024-01-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [173] " purrr 1.0.2 \033[90m2023-08-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [174] " R6 2.5.1 \033[90m2021-08-19\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [175] " ragg 1.2.7 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [176] " RANN 2.6.1 \033[90m2019-01-08\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [177] " rappdirs 0.3.3 \033[90m2021-01-31\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [178] " RColorBrewer 1.1-3 \033[90m2022-04-03\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [179] " Rcpp 1.0.12 \033[90m2024-01-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [180] " RcppAnnoy 0.0.22 \033[90m2024-01-23\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [181] " RcppHNSW 0.6.0 \033[90m2024-02-04\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [182] " RCurl 1.98-1.14 \033[90m2024-01-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [183] " readr 2.1.5 \033[90m2024-01-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [184] " remotes 2.4.2.1 \033[90m2023-07-18\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [185] " reshape2 1.4.4 \033[90m2020-04-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [186] " restfulr 0.0.15 \033[90m2022-06-16\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [187] " reticulate 1.35.0 \033[90m2024-01-31\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [188] " rhandsontable 0.3.8 \033[90m2021-05-27\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [189] " rhdf5 2.47.2 \033[90m2024-01-15\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [190] " rhdf5filters 1.15.2 \033[90m2024-02-02\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [191] " Rhdf5lib 1.25.1 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [192] " rjson 0.2.21 \033[90m2022-01-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [193] " rlang 1.1.3 \033[90m2024-01-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [194] " rmarkdown 2.25 \033[90m2023-09-18\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [195] " ROCR 1.0-11 \033[90m2020-05-02\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [196] " Rsamtools 2.19.3 \033[90m2024-01-17\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [197] " RSpectra 0.16-1 \033[90m2022-04-24\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [198] " RSQLite 2.3.5 \033[90m2024-01-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [199] " rstudioapi 0.15.0 \033[90m2023-07-07\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [200] " rsvd 1.0.5 \033[90m2021-04-16\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [201] " rtracklayer 1.63.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [202] " Rtsne 0.17 \033[90m2023-12-07\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [203] " S4Arrays 1.3.3 \033[90m2024-01-31\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [204] " S4Vectors * 0.41.3 \033[90m2024-01-01\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [205] " sass 0.4.8 \033[90m2023-12-06\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [206] " ScaledMatrix 1.11.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [207] " scales 1.3.0 \033[90m2023-11-28\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [208] " scater 1.31.2 \033[90m2024-01-28\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [209] " scattermore 1.2 \033[90m2023-06-12\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [210] " scran 1.31.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [211] " sctransform 0.4.1 \033[90m2023-10-19\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [212] " scuttle 1.13.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [213] " sessioninfo 1.2.2 \033[90m2021-12-06\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [214] " Seurat * 5.0.1 \033[90m2023-11-17\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [215] " SeuratObject * 5.0.1 \033[90m2023-11-17\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [216] " seuratTools * 0.6.0 \033[90m2024-06-14\033[39m \033[90m[1]\033[39m \033[90mBioconductor\033[39m"
#> [217] " shiny * 1.8.0 \033[90m2023-11-17\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [218] " shinyBS 0.61.1 \033[90m2022-04-17\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [219] " shinydashboard * 0.7.2 \033[90m2021-09-30\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [220] " shinyjs 2.1.0 \033[90m2021-12-23\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [221] " SingleCellExperiment * 1.25.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [222] " sp * 2.1-3 \033[90m2024-01-30\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [223] " spam 2.10-0 \033[90m2023-10-23\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [224] " SparseArray 1.3.4 \033[90m2024-02-11\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [225] " sparseMatrixStats 1.15.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [226] " spatstat.data 3.0-4 \033[90m2024-01-15\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [227] " spatstat.explore 3.2-6 \033[90m2024-02-01\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [228] " spatstat.geom 3.2-8 \033[90m2024-01-26\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [229] " spatstat.random 3.2-2 \033[90m2023-11-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [230] " spatstat.sparse 3.0-3 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [231] " spatstat.utils 3.0-4 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [232] " statmod 1.5.0 \033[90m2023-01-06\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [233] " stringi 1.8.3 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [234] " stringr 1.5.1 \033[90m2023-11-14\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [235] " SummarizedExperiment * 1.33.3 \033[90m2024-01-23\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [236] " survival 3.5-7 \033[90m2023-08-14\033[39m \033[90m[3]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [237] " systemfonts 1.0.5 \033[90m2023-10-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [238] " tensor 1.5 \033[90m2012-05-05\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [239] " terra 1.7-71 \033[90m2024-01-31\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [240] " textshaping 0.3.7 \033[90m2023-10-09\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [241] " tibble 3.2.1 \033[90m2023-03-20\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [242] " tidygraph 1.2.3 \033[90m2023-02-01\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [243] " tidyr 1.3.1 \033[90m2024-01-24\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [244] " tidyselect 1.2.0 \033[90m2022-10-10\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [245] " tidyverse 2.0.0 \033[90m2023-02-22\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [246] " timechange 0.3.0 \033[90m2024-01-18\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [247] " tweenr 2.0.3 \033[90m2024-02-26\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [248] " tzdb 0.4.0 \033[90m2023-05-12\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [249] " urlchecker 1.0.1 \033[90m2021-11-30\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [250] " usethis 2.2.3 \033[90m2024-02-19\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [251] " utf8 1.2.4 \033[90m2023-10-22\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [252] " uwot 0.1.16 \033[90m2023-06-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [253] " vctrs 0.6.5 \033[90m2023-12-01\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [254] " velociraptor 1.13.1 \033[90m2024-01-30\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [255] " vipor 0.4.7 \033[90m2023-12-18\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [256] " viridis 0.6.5 \033[90m2024-01-29\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [257] " viridisLite 0.4.2 \033[90m2023-05-02\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [258] " whisker 0.4.1 \033[90m2022-12-05\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [259] " withr 3.0.0 \033[90m2024-01-16\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [260] " xfun 0.42 \033[90m2024-02-08\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [261] " XML 3.99-0.16.1 \033[90m2024-01-22\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [262] " xml2 1.3.6 \033[90m2023-12-04\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [263] " xtable 1.8-4 \033[90m2019-04-21\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [264] " XVector 0.43.1 \033[90m2024-01-10\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [265] " yaml 2.3.8 \033[90m2023-12-11\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.4.0)\033[39m"
#> [266] " zellkonverter 1.13.2 \033[90m2024-01-17\033[39m \033[90m[2]\033[39m \033[90mBioconductor 3.19 (R 4.4.0)\033[39m"
#> [267] " zlibbioc 1.49.0 \033[90m2023-10-24\033[39m \033[90m[2]\033[39m \033[90mBioconductor\033[39m"
#> [268] " zoo 1.8-12 \033[90m2023-04-13\033[39m \033[90m[2]\033[39m \033[90mCRAN (R 4.3.1)\033[39m"
#> [269] ""
#> [270] "\033[90m [1] /tmp/RtmpTL487d/temp_libpath31eec93832e935\033[39m"
#> [271] "\033[90m [2] /dataVolume/R/devel/site-library\033[39m"
#> [272] "\033[90m [3] /opt/R/devel/lib/R/library\033[39m"
#> [273] ""
#> [274] "\033[1m\033[36m──────────────────────────────────────────────────────────────────────────────\033[39m\033[22m"
#>
#>
#> $seurat_version
#> [1] '5.0.0'
#>
#> $seuratTools_version
#> [1] '0.6.0'
#>