Last updated: 2021-11-08

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Knit directory: single-cell-topics/analysis/

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Rmd 71e267d Peter Carbonetto 2021-11-08 workflowr::wflow_publish(“index.Rmd”)

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