The running environment for generating this tutorial:
sessionInfo()
## R version 3.6.2 (2019-12-12)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS: /cm/shared/apps_chop/R/3.6.2/lib64/R/lib/libRblas.so
## LAPACK: /cm/shared/apps_chop/R/3.6.2/lib64/R/lib/libRlapack.so
##
## 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=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## attached base packages:
## [1] grid splines compiler parallel stats4 stats graphics grDevices
## [9] utils datasets methods base
##
## other attached packages:
## [1] cicero_1.4.0 Gviz_1.28.3
## [3] monocle_2.14.0 DDRTree_0.1.5
## [5] irlba_2.3.3 VGAM_1.1-2
## [7] Matrix_1.2-18 kableExtra_1.1.0
## [9] xlsx_0.6.2 mclust_5.4.5
## [11] edgeR_3.26.8 limma_3.42.2
## [13] readr_1.3.1 SummarizedExperiment_1.16.1
## [15] DelayedArray_0.12.2 BiocParallel_1.20.1
## [17] matrixStats_0.55.0 Biobase_2.46.0
## [19] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0
## [21] IRanges_2.20.2 S4Vectors_0.24.4
## [23] BiocGenerics_0.32.0 motifmatchr_1.8.0
## [25] chromVAR_1.8.0 pheatmap_1.0.12
## [27] viridis_0.5.1 viridisLite_0.3.0
## [29] RColorBrewer_1.1-2 Seurat_3.1.5
## [31] ggplot2_3.2.1 magrittr_1.5
## [33] data.table_1.12.8
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.1 rtracklayer_1.44.4
## [3] R.methodsS3_1.8.0 tidyr_1.0.2
## [5] acepack_1.4.1 bit64_0.9-7
## [7] knitr_1.28 R.utils_2.9.2
## [9] rpart_4.1-15 AnnotationFilter_1.8.0
## [11] KEGGREST_1.26.1 TFBSTools_1.24.0
## [13] RCurl_1.98-1.1 GenomicFeatures_1.36.4
## [15] callr_3.4.2 cowplot_1.0.0
## [17] usethis_1.5.1 RSQLite_2.2.0
## [19] RANN_2.6.1 combinat_0.0-8
## [21] future_1.16.0 bit_1.1-15.2
## [23] webshot_0.5.2 xml2_1.2.2
## [25] httpuv_1.5.2 assertthat_0.2.1
## [27] DirichletMultinomial_1.28.0 xfun_0.12
## [29] hms_0.5.2 rJava_0.9-11
## [31] evaluate_0.14 promises_1.1.0
## [33] fansi_0.4.1 progress_1.2.2
## [35] caTools_1.18.0 igraph_1.2.4.2
## [37] DBI_1.1.0 htmlwidgets_1.5.1
## [39] sparsesvd_0.2 purrr_0.3.3
## [41] RSpectra_0.16-0 dplyr_0.8.4
## [43] backports_1.1.5 annotate_1.64.0
## [45] RcppParallel_4.4.4 biomaRt_2.40.5
## [47] vctrs_0.2.2 ensembldb_2.8.1
## [49] remotes_2.1.1 ROCR_1.0-7
## [51] withr_2.1.2 packrat_0.5.0
## [53] BSgenome_1.54.0 checkmate_1.9.4
## [55] sctransform_0.2.1 GenomicAlignments_1.22.1
## [57] prettyunits_1.1.1 cluster_2.1.0
## [59] ape_5.3 lazyeval_0.2.2
## [61] seqLogo_1.52.0 crayon_1.3.4
## [63] pkgconfig_2.0.3 slam_0.1-46
## [65] labeling_0.3 ProtGenerics_1.16.0
## [67] nlme_3.1-143 pkgload_1.0.2
## [69] nnet_7.3-12 devtools_2.1.0
## [71] rlang_0.4.4 globals_0.12.5
## [73] lifecycle_0.1.0 miniUI_0.1.1.1
## [75] rsvd_1.0.3 dichromat_2.0-0
## [77] rprojroot_1.3-2 lmtest_0.9-37
## [79] zoo_1.8-7 base64enc_0.1-3
## [81] ggridges_0.5.2 processx_3.4.2
## [83] png_0.1-7 bitops_1.0-6
## [85] R.oo_1.23.0 KernSmooth_2.23-16
## [87] Biostrings_2.54.0 blob_1.2.1
## [89] stringr_1.4.0 CNEr_1.22.0
## [91] scales_1.1.0 memoise_1.1.0
## [93] plyr_1.8.5 ica_1.0-2
## [95] gplots_3.0.1.2 gdata_2.18.0
## [97] zlibbioc_1.32.0 HSMMSingleCell_1.4.0
## [99] lsei_1.2-0 fitdistrplus_1.0-14
## [101] Rsamtools_2.0.3 cli_2.0.1
## [103] XVector_0.26.0 listenv_0.8.0
## [105] patchwork_1.0.0 pbapply_1.4-2
## [107] ps_1.3.2 htmlTable_1.13.1
## [109] Formula_1.2-3 MASS_7.3-51.5
## [111] tidyselect_1.0.0 stringi_1.4.6
## [113] highr_0.8 densityClust_0.3
## [115] yaml_2.2.1 locfit_1.5-9.1
## [117] latticeExtra_0.6-28 ggrepel_0.8.1
## [119] VariantAnnotation_1.30.1 tools_3.6.2
## [121] future.apply_1.4.0 rstudioapi_0.11
## [123] TFMPvalue_0.0.8 foreign_0.8-74
## [125] gridExtra_2.3 farver_2.0.3
## [127] Rtsne_0.15 digest_0.6.24
## [129] FNN_1.1.3 shiny_1.4.0
## [131] qlcMatrix_0.9.7 Rcpp_1.0.3
## [133] later_1.0.0 RcppAnnoy_0.0.14
## [135] httr_1.4.1 AnnotationDbi_1.48.0
## [137] biovizBase_1.32.0 npsurv_0.4-0
## [139] colorspace_1.4-1 rvest_0.3.5
## [141] XML_3.99-0.3 fs_1.3.1
## [143] reticulate_1.14 uwot_0.1.5
## [145] xlsxjars_0.6.1 plotly_4.9.2
## [147] sessioninfo_1.1.1 xtable_1.8-4
## [149] jsonlite_1.6.1 poweRlaw_0.70.2
## [151] testthat_2.2.1 R6_2.4.1
## [153] Hmisc_4.2-0 pillar_1.4.2
## [155] htmltools_0.4.0 mime_0.9
## [157] glue_1.3.1 fastmap_1.0.1
## [159] DT_0.9 codetools_0.2-16
## [161] pkgbuild_1.0.5 tsne_0.1-3
## [163] lattice_0.20-38 tibble_2.1.3
## [165] curl_4.3 leiden_0.3.3
## [167] gtools_3.8.1 GO.db_3.10.0
## [169] survival_3.1-8 rmarkdown_2.1
## [171] docopt_0.6.1 desc_1.2.0
## [173] fastICA_1.2-2 munsell_0.5.0
## [175] GenomeInfoDbData_1.2.2 reshape2_1.4.3
## [177] gtable_0.3.0