Last updated: 2021-11-08
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Knit directory: single-cell-topics/analysis/
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TO DO: Give overview of analysis here.
Load the packages used in the analysis below, as well as additional functions that we will use to generate some of the plots.
library(Matrix)
library(fastTopics)
library(ggplot2)
library(cowplot)
sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
#
# Matrix products: default
# BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] cowplot_1.0.0 ggplot2_3.3.5 fastTopics_0.6-74 Matrix_1.2-18
#
# loaded via a namespace (and not attached):
# [1] httr_1.4.2 tidyr_1.1.3 jsonlite_1.7.2 viridisLite_0.3.0
# [5] RcppParallel_4.4.2 assertthat_0.2.1 mixsqp_0.3-46 yaml_2.2.0
# [9] progress_1.2.2 ggrepel_0.9.1 pillar_1.6.2 backports_1.1.5
# [13] lattice_0.20-38 quantreg_5.54 glue_1.4.2 quadprog_1.5-8
# [17] digest_0.6.23 promises_1.1.0 colorspace_1.4-1 htmltools_0.4.0
# [21] httpuv_1.5.2 pkgconfig_2.0.3 invgamma_1.1 SparseM_1.78
# [25] purrr_0.3.4 scales_1.1.0 whisker_0.4 later_1.0.0
# [29] Rtsne_0.15 MatrixModels_0.4-1 git2r_0.26.1 tibble_3.1.3
# [33] generics_0.0.2 ellipsis_0.3.2 withr_2.4.2 ashr_2.2-51
# [37] pbapply_1.5-1 lazyeval_0.2.2 magrittr_2.0.1 crayon_1.4.1
# [41] mcmc_0.9-6 evaluate_0.14 fs_1.3.1 fansi_0.4.0
# [45] MASS_7.3-51.4 truncnorm_1.0-8 tools_3.6.2 data.table_1.12.8
# [49] prettyunits_1.1.1 hms_1.1.0 lifecycle_1.0.0 stringr_1.4.0
# [53] MCMCpack_1.4-5 plotly_4.9.2 munsell_0.5.0 irlba_2.3.3
# [57] compiler_3.6.2 rlang_0.4.11 grid_3.6.2 htmlwidgets_1.5.1
# [61] rmarkdown_2.3 gtable_0.3.0 DBI_1.1.0 R6_2.4.1
# [65] knitr_1.26 dplyr_1.0.7 utf8_1.1.4 workflowr_1.6.2
# [69] rprojroot_1.3-2 stringi_1.4.3 parallel_3.6.2 SQUAREM_2017.10-1
# [73] Rcpp_1.0.7 vctrs_0.3.8 tidyselect_1.1.1 xfun_0.11
# [77] coda_0.19-3