Prior to the workshop, please complete the following:

Download the data

Please download the data in data.zip. Then, move data.zip to your Desktop and unzip it (usually double-clicking it will work).

If the above link does not work, please try downloading the data with Download button at https://github.com/BIGslu/workshops/blob/main/2022.08.15_R.tidyverse.workshop/data/data.zip.

Install R and RStudio

When you open RStudio, it should look like so with multiple panels. If you see only 1 panel, then you’re likely in R, not RStudio.

Install R packages

Install R packages by running the following script in your R console (left panel in the above image).

#CRAN packages
install.packages("tidyverse")
install.packages("ggrepel")
#Bioconductor packages
install.packages("BiocManager")
BiocManager::install("limma")

If prompted, say a to “Update all/some/none? [a/s/n]” and no to “Do you want to install from sources the packages which need compilation? (Yes/no/cancel)”

This can take several minutes.

Check R package install

To make sure packages are correctly installed, load them into R with library( ). If you see any ERROR, please come 15 minutes early to the workshop the day of or contact Kim for assistance.

First, the package(s) that give messages upon loading.

library(tidyverse)
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.3.6     ✔ purrr   0.3.4
## ✔ tibble  3.1.8     ✔ dplyr   1.0.9
## ✔ tidyr   1.2.0     ✔ stringr 1.4.0
## ✔ readr   2.1.2     ✔ forcats 0.5.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()

Then, check package(s) that load silently with no messages.

library(limma)
library(ggrepel)

R package versions

For reproducibility, here is the complete list of software used in this workshop.

sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## 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] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ggrepel_0.9.1   limma_3.52.2    forcats_0.5.1   stringr_1.4.0  
##  [5] dplyr_1.0.9     purrr_0.3.4     readr_2.1.2     tidyr_1.2.0    
##  [9] tibble_3.1.8    ggplot2_3.3.6   tidyverse_1.3.2
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9          lubridate_1.8.0     assertthat_0.2.1   
##  [4] rprojroot_2.0.3     digest_0.6.29       utf8_1.2.2         
##  [7] R6_2.5.1            cellranger_1.1.0    backports_1.4.1    
## [10] reprex_2.0.1        evaluate_0.15       httr_1.4.3         
## [13] pillar_1.8.0        rlang_1.0.4         googlesheets4_1.0.0
## [16] readxl_1.4.0        rstudioapi_0.13     jquerylib_0.1.4    
## [19] rmarkdown_2.14      googledrive_2.0.0   munsell_0.5.0      
## [22] broom_1.0.0         compiler_4.2.1      modelr_0.1.8       
## [25] xfun_0.31           pkgconfig_2.0.3     htmltools_0.5.3    
## [28] tidyselect_1.1.2    fansi_1.0.3         crayon_1.5.1       
## [31] tzdb_0.3.0          dbplyr_2.2.1        withr_2.5.0        
## [34] grid_4.2.1          jsonlite_1.8.0      gtable_0.3.0       
## [37] lifecycle_1.0.1     DBI_1.1.3           magrittr_2.0.3     
## [40] scales_1.2.0        cli_3.3.0           stringi_1.7.8      
## [43] cachem_1.0.6        fs_1.5.2            xml2_1.3.3         
## [46] bslib_0.4.0         ellipsis_0.3.2      generics_0.1.3     
## [49] vctrs_0.4.1         tools_4.2.1         glue_1.6.2         
## [52] hms_1.1.1           fastmap_1.1.0       yaml_2.3.5         
## [55] colorspace_2.0-3    gargle_1.2.0        rvest_1.0.2        
## [58] knitr_1.39          haven_2.5.0         sass_0.4.2