Chapter 5 About this project
Session Information
## R version 4.2.1 (2022-06-23)
## 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 VGAM_1.1-9 Matrix_1.5-3
## [6] SeuratObject_4.1.3 Seurat_4.3.0 GSEABase_1.58.0 graph_1.74.0 annotate_1.74.0
## [11] XML_3.99-0.14 enrichplot_1.16.2 ggthemes_4.2.4 org.Hs.eg.db_3.15.0 AnnotationDbi_1.58.0
## [16] GSVA_1.44.5 genefilter_1.78.0 clusterProfiler_4.4.4 randomForest_4.7-1.1 limma_3.52.4
## [21] ggpubr_0.6.0 dendextend_1.17.1 openxlsx_4.2.5.2 DESeq2_1.36.0 SummarizedExperiment_1.32.0
## [26] Biobase_2.56.0 MatrixGenerics_1.14.0 matrixStats_1.0.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4
## [31] IRanges_2.30.1 S4Vectors_0.34.0 BiocGenerics_0.44.0 ggplot2_3.4.4 pheatmap_1.0.12
## [36] e1071_1.7-13 dplyr_1.1.3
##
## loaded via a namespace (and not attached):
## [1] scattermore_1.2 tidyr_1.3.0 bit64_4.0.5 knitr_1.44 DelayedArray_0.28.0
## [6] data.table_1.14.8 KEGGREST_1.36.3 RCurl_1.98-1.12 generics_0.1.3 ScaledMatrix_1.4.1
## [11] leidenbase_0.1.25 cowplot_1.1.1 RSQLite_2.2.18 combinat_0.0-8 shadowtext_0.1.2
## [16] RANN_2.6.1 proxy_0.4-27 future_1.33.0 bit_4.0.5 spatstat.data_3.0-3
## [21] httpuv_1.6.9 viridis_0.6.4 xfun_0.40 jquerylib_0.1.4 evaluate_0.22
## [26] promises_1.2.1 fansi_1.0.5 igraph_1.5.1 DBI_1.1.3 geneplotter_1.74.0
## [31] htmlwidgets_1.6.2 sparsesvd_0.2-2 spatstat.geom_3.2-7 purrr_1.0.2 ellipsis_0.3.2
## [36] backports_1.4.1 bookdown_0.36 deldir_1.0-9 sparseMatrixStats_1.8.0 vctrs_0.6.4
## [41] SingleCellExperiment_1.18.1 ROCR_1.0-11 abind_1.4-5 cachem_1.0.8 withr_2.5.1
## [46] ggforce_0.4.1 progressr_0.14.0 sctransform_0.4.1 treeio_1.20.2 goftest_1.2-3
## [51] cluster_2.1.4 DOSE_3.22.1 ape_5.7-1 lazyeval_0.2.2 crayon_1.5.2
## [56] spatstat.explore_3.1-0 slam_0.1-50 pkgconfig_2.0.3 tweenr_2.0.2 nlme_3.1-163
## [61] rlang_1.1.1 globals_0.16.2 lifecycle_1.0.3 miniUI_0.1.1.1 downloader_0.4
## [66] rsvd_1.0.5 polyclip_1.10-6 lmtest_0.9-40 aplot_0.2.2 carData_3.0-5
## [71] Rhdf5lib_1.18.2 zoo_1.8-12 ggridges_0.5.4 png_0.1-8 viridisLite_0.4.2
## [76] bitops_1.0-7 KernSmooth_2.23-22 rhdf5filters_1.8.0 Biostrings_2.64.1 blob_1.2.4
## [81] DelayedMatrixStats_1.18.2 stringr_1.5.0 qvalue_2.28.0 spatstat.random_3.2-1 parallelly_1.36.0
## [86] rstatix_0.7.2 gridGraphics_0.5-1 ggsignif_0.6.4 beachmat_2.18.0 scales_1.2.1
## [91] memoise_2.0.1 magrittr_2.0.3 plyr_1.8.9 ica_1.0-3 zlibbioc_1.42.0
## [96] HSMMSingleCell_1.16.0 compiler_4.2.1 scatterpie_0.2.1 RColorBrewer_1.1-3 fitdistrplus_1.1-11
## [101] cli_3.6.1 XVector_0.36.0 listenv_0.9.0 patchwork_1.1.3 pbapply_1.7-2
## [106] MASS_7.3-60 tidyselect_1.2.0 stringi_1.7.12 yaml_2.3.7 GOSemSim_2.22.0
## [111] BiocSingular_1.12.0 locfit_1.5-9.8 ggrepel_0.9.4 grid_4.2.1 sass_0.4.7
## [116] fastmatch_1.1-4 tools_4.2.1 future.apply_1.11.0 parallel_4.2.1 rstudioapi_0.15.0
## [121] gridExtra_2.3 farver_2.1.1 Rtsne_0.16 ggraph_2.1.0 digest_0.6.33
## [126] shiny_1.7.5.1 qlcMatrix_0.9.7 Rcpp_1.0.11 car_3.1-2 broom_1.0.5
## [131] later_1.3.1 RcppAnnoy_0.0.21 httr_1.4.7 colorspace_2.1-0 tensor_1.5
## [136] fs_1.6.3 reticulate_1.34.0 uwot_0.1.16 yulab.utils_0.1.0 tidytree_0.4.5
## [141] SparseArray_1.2.0 spatstat.utils_3.0-2 graphlayouts_1.0.1 sp_2.1-1 ggplotify_0.1.2
## [146] plotly_4.10.3 xtable_1.8-4 jsonlite_1.8.7 ggtree_3.4.4 tidygraph_1.2.3
## [151] ggfun_0.1.3 R6_2.5.1 S4Arrays_1.2.0 pillar_1.9.0 htmltools_0.5.6.1
## [156] mime_0.12 glue_1.6.2 fastmap_1.1.1 BiocParallel_1.30.4 class_7.3-22
## [161] codetools_0.2-19 fgsea_1.22.0 utf8_1.2.3 spatstat.sparse_3.0-1 lattice_0.20-45
## [166] bslib_0.5.1 tibble_3.2.1 leiden_0.4.3 zip_2.3.0 GO.db_3.15.0
## [171] survival_3.5-7 docopt_0.7.1 rmarkdown_2.25 fastICA_1.2-3 munsell_0.5.0
## [176] DO.db_2.9 rhdf5_2.40.0 GenomeInfoDbData_1.2.8 HDF5Array_1.24.2 reshape2_1.4.4
## [181] gtable_0.3.4