Prior to the workshop, please complete the following:

Download the data

Please download the data in 0_data.zip. Then, move 0_data.zip to your Desktop and unzip it (usually double-clicking it will work).

All workshop material and data are available at https://github.com/BIGslu/2022_ASM_Microbe_RNAseq.

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(c("tidyverse", "lme4", "lmerTest"))

#Bioconductor packages
install.packages("BiocManager")
BiocManager::install(c("edgeR", "biomaRt", "limma"))

#GitHub packages
install.packages("devtools")
devtools::install_github("BIGslu/RNAetc")
devtools::install_github("BIGslu/kimma")

Check R package install

To make sure packages are correctly installed, load them into R with library( ). If you see any ERROR, please attend office hours the day before the workshop (information sent in the setup email) or come 15 minutes early to the workshop the day of.

First, the three packages that give messages upon loading.

library(tidyverse)
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
## ✔ ggplot2 3.3.6     ✔ purrr   0.3.4
## ✔ tibble  3.1.7     ✔ dplyr   1.0.8
## ✔ 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()
library(edgeR)
## Loading required package: limma
## Warning: package 'limma' was built under R version 4.1.3
library(lme4)
## Loading required package: Matrix
## 
## Attaching package: 'Matrix'
## The following objects are masked from 'package:tidyr':
## 
##     expand, pack, unpack
library(lmerTest)
## 
## Attaching package: 'lmerTest'
## The following object is masked from 'package:lme4':
## 
##     lmer
## The following object is masked from 'package:stats':
## 
##     step

Then, four packages that load silently with no messages.

library(biomaRt)
library(limma)
library(RNAetc)
library(kimma)

R package versions

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

sessionInfo()
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] kimma_1.3.0     RNAetc_0.1.0    biomaRt_2.50.3  lmerTest_3.1-3 
##  [5] lme4_1.1-29     Matrix_1.4-0    edgeR_3.36.0    limma_3.50.3   
##  [9] forcats_0.5.1   stringr_1.4.0   dplyr_1.0.8     purrr_0.3.4    
## [13] readr_2.1.2     tidyr_1.2.0     tibble_3.1.7    ggplot2_3.3.6  
## [17] tidyverse_1.3.1
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-155           bitops_1.0-7           fs_1.5.2              
##  [4] lubridate_1.8.0        bit64_4.0.5            filelock_1.0.2        
##  [7] progress_1.2.2         httr_1.4.2             GenomeInfoDb_1.30.1   
## [10] rprojroot_2.0.3        numDeriv_2016.8-1.1    tools_4.1.2           
## [13] backports_1.4.1        bslib_0.3.1            utf8_1.2.2            
## [16] R6_2.5.1               DBI_1.1.2              BiocGenerics_0.40.0   
## [19] colorspace_2.0-3       withr_2.5.0            prettyunits_1.1.1     
## [22] tidyselect_1.1.2       curl_4.3.2             bit_4.0.4             
## [25] compiler_4.1.2         cli_3.3.0              rvest_1.0.2           
## [28] Biobase_2.54.0         xml2_1.3.3             sass_0.4.0            
## [31] scales_1.2.0           rappdirs_0.3.3         digest_0.6.29         
## [34] minqa_1.2.4            rmarkdown_2.11         XVector_0.34.0        
## [37] pkgconfig_2.0.3        htmltools_0.5.2        dbplyr_2.1.1          
## [40] fastmap_1.1.0          rlang_1.0.2            readxl_1.3.1          
## [43] rstudioapi_0.13        RSQLite_2.2.12         jquerylib_0.1.4       
## [46] generics_0.1.2         jsonlite_1.8.0         RCurl_1.98-1.6        
## [49] magrittr_2.0.3         GenomeInfoDbData_1.2.7 Rcpp_1.0.8.3          
## [52] munsell_0.5.0          S4Vectors_0.32.4       fansi_1.0.3           
## [55] lifecycle_1.0.1        stringi_1.7.6          yaml_2.3.5            
## [58] zlibbioc_1.40.0        MASS_7.3-55            BiocFileCache_2.2.1   
## [61] grid_4.1.2             blob_1.2.3             crayon_1.5.1          
## [64] lattice_0.20-45        Biostrings_2.62.0      haven_2.4.3           
## [67] splines_4.1.2          KEGGREST_1.34.0        hms_1.1.1             
## [70] locfit_1.5-9.5         knitr_1.39             pillar_1.7.0          
## [73] boot_1.3-28            codetools_0.2-18       stats4_4.1.2          
## [76] reprex_2.0.1           XML_3.99-0.8           glue_1.6.2            
## [79] evaluate_0.15          modelr_0.1.8           foreach_1.5.2         
## [82] png_0.1-7              vctrs_0.4.1            nloptr_2.0.0          
## [85] tzdb_0.3.0             cellranger_1.1.0       gtable_0.3.0          
## [88] assertthat_0.2.1       cachem_1.0.6           xfun_0.30             
## [91] broom_0.8.0            iterators_1.0.14       IRanges_2.28.0        
## [94] AnnotationDbi_1.56.2   memoise_2.0.1          ellipsis_0.3.2