Chapter 5 About this project
Session Information
## R version 4.0.3
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Ventura 13.0.1
##
## Matrix products: default
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] splines stats4 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] monocle_2.24.1 DDRTree_0.1.5 irlba_2.3.5.1
## [4] VGAM_1.1-7 Matrix_1.5-3 SeuratObject_4.1.3
## [7] Seurat_4.3.0 GSEABase_1.58.0 graph_1.74.0
## [10] annotate_1.74.0 XML_3.99-0.12 AnnotationDbi_1.58.0
## [13] enrichplot_1.16.2 GSVA_1.44.5 genefilter_1.78.0
## [16] clusterProfiler_4.4.4 randomForest_4.7-1.1 limma_3.52.4
## [19] ggpubr_0.5.0 dendextend_1.16.0 openxlsx_4.2.5.1
## [22] DESeq2_1.36.0 SummarizedExperiment_1.26.1 Biobase_2.56.0
## [25] MatrixGenerics_1.8.1 matrixStats_0.63.0 GenomicRanges_1.48.0
## [28] GenomeInfoDb_1.32.4 IRanges_2.30.1 S4Vectors_0.34.0
## [31] BiocGenerics_0.42.0 pheatmap_1.0.12 dplyr_1.1.2
## [34] ggplot2_3.4.3 ggthemes_4.2.4 connector_0.0.0.9000
##
## loaded via a namespace (and not attached):
## [1] scattermore_0.8 tidyr_1.3.0 bit64_4.0.5
## [4] knitr_1.42 DelayedArray_0.22.0 data.table_1.14.8
## [7] KEGGREST_1.36.3 RCurl_1.98-1.9 generics_0.1.3
## [10] ScaledMatrix_1.4.1 leidenbase_0.1.14 cowplot_1.1.1
## [13] shinybusy_0.3.1 RSQLite_2.2.18 combinat_0.0-8
## [16] shadowtext_0.1.2 RANN_2.6.1 future_1.32.0
## [19] bit_4.0.5 spatstat.data_3.0-1 httpuv_1.6.9
## [22] isoband_0.2.7 viridis_0.6.4 xfun_0.39
## [25] jquerylib_0.1.4 evaluate_0.20 promises_1.2.0.1
## [28] fansi_1.0.4 readxl_1.4.3 igraph_1.4.2
## [31] DBI_1.1.3 geneplotter_1.74.0 htmlwidgets_1.6.2
## [34] sparsesvd_0.2-2 spatstat.geom_3.1-0 purrr_1.0.1
## [37] ellipsis_0.3.2 ks_1.14.1 backports_1.4.1
## [40] bookdown_0.32 markdown_1.6 deldir_1.0-6
## [43] sparseMatrixStats_1.8.0 vctrs_0.6.2 SingleCellExperiment_1.18.1
## [46] ROCR_1.0-11 abind_1.4-5 cachem_1.0.7
## [49] withr_2.5.0 ggforce_0.4.1 sfsmisc_1.1-16
## [52] progressr_0.13.0 sctransform_0.3.5 treeio_1.20.2
## [55] goftest_1.2-3 mclust_6.0.0 cluster_2.1.4
## [58] DOSE_3.22.1 ape_5.6-2 lazyeval_0.2.2
## [61] crayon_1.5.2 spatstat.explore_3.1-0 slam_0.1-50
## [64] pkgconfig_2.0.3 labeling_0.4.2 tweenr_2.0.2
## [67] nlme_3.1-160 globals_0.16.2 rlang_1.1.0
## [70] miniUI_0.1.1.1 lifecycle_1.0.3 downloader_0.4
## [73] rsvd_1.0.5 cellranger_1.1.0 polyclip_1.10-4
## [76] lmtest_0.9-40 shinyFiles_0.9.3 aplot_0.1.8
## [79] carData_3.0-5 zoo_1.8-12 Rhdf5lib_1.18.2
## [82] ggridges_0.5.4 png_0.1-8 viridisLite_0.4.1
## [85] bitops_1.0-7 shinydashboard_0.7.2 KernSmooth_2.23-20
## [88] rhdf5filters_1.8.0 Biostrings_2.64.1 blob_1.2.3
## [91] DelayedMatrixStats_1.18.2 stringr_1.5.0 qvalue_2.28.0
## [94] spatstat.random_3.1-4 parallelly_1.35.0 rstatix_0.7.1
## [97] gridGraphics_0.5-1 ggsignif_0.6.4 beachmat_2.12.0
## [100] scales_1.2.1 ica_1.0-3 memoise_2.0.1
## [103] magrittr_2.0.3 plyr_1.8.8 zlibbioc_1.42.0
## [106] HSMMSingleCell_1.16.0 compiler_4.2.1 hdrcde_3.4
## [109] scatterpie_0.1.8 RColorBrewer_1.1-3 fitdistrplus_1.1-8
## [112] cli_3.6.1 XVector_0.36.0 listenv_0.9.0
## [115] pbapply_1.7-0 patchwork_1.1.2 mgcv_1.8-41
## [118] MASS_7.3-60 tidyselect_1.2.0 stringi_1.7.12
## [121] highr_0.10 yaml_2.3.7 GOSemSim_2.22.0
## [124] BiocSingular_1.12.0 locfit_1.5-9.8 ggrepel_0.9.3
## [127] grid_4.2.1 sass_0.4.5 fastmatch_1.1-3
## [130] tools_4.2.1 future.apply_1.10.0 parallel_4.2.1
## [133] rstudioapi_0.14 gridExtra_2.3 farver_2.1.1
## [136] Rtsne_0.16 ggraph_2.1.0 digest_0.6.31
## [139] shiny_1.7.4 pracma_2.4.2 qlcMatrix_0.9.7
## [142] Rcpp_1.0.10 car_3.1-1 broom_1.0.1
## [145] later_1.3.0 RcppAnnoy_0.0.20 fda_6.1.4
## [148] shinyWidgets_0.7.6 httr_1.4.5 colorspace_2.1-0
## [151] tensor_1.5 reticulate_1.28 fs_1.6.1
## [154] rainbow_3.7 uwot_0.1.14 yulab.utils_0.0.5
## [157] statmod_1.5.0 spatstat.utils_3.0-2 tidytree_0.4.1
## [160] graphlayouts_0.8.3 sp_1.6-0 ggplotify_0.1.2
## [163] plotly_4.10.1 xtable_1.8-4 jsonlite_1.8.4
## [166] ggtree_3.4.4 fds_1.8 tidygraph_1.2.2
## [169] ggfun_0.0.8 R6_2.5.1 pillar_1.9.0
## [172] htmltools_0.5.5 mime_0.12 glue_1.6.2
## [175] fastmap_1.1.1 BiocParallel_1.30.4 deSolve_1.36
## [178] codetools_0.2-18 fgsea_1.22.0 pcaPP_2.0-3
## [181] mvtnorm_1.1-3 utf8_1.2.3 spatstat.sparse_3.0-1
## [184] lattice_0.20-45 bslib_0.4.2 tibble_3.2.1
## [187] leiden_0.4.3 dashboardthemes_1.1.6 zip_2.2.2
## [190] GO.db_3.15.0 shinyjs_2.1.0 survival_3.4-0
## [193] docopt_0.7.1 rmarkdown_2.21 fastICA_1.2-3
## [196] munsell_0.5.0 DO.db_2.9 rhdf5_2.40.0
## [199] GenomeInfoDbData_1.2.8 HDF5Array_1.24.2 reshape2_1.4.4
## [202] gtable_0.3.3