Last updated: 2021-07-07

Checks: 7 0

Knit directory: Bulk_RNAseq/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20210629) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 382c838. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    output/.DS_Store
    Ignored:    renv/library/
    Ignored:    renv/local/
    Ignored:    renv/staging/

Untracked files:
    Untracked:  code/
    Untracked:  rlib/

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 382c838 Nhi Hin 2021-07-07 wflow_publish(“analysis/index.Rmd”)
html 164b09e Nhi Hin 2021-07-07 Build site.
Rmd 4b869d7 Nhi Hin 2021-07-07 wflow_publish(“analysis/index.Rmd”)
html 7e2fbf0 Nhi Hin 2021-07-02 Build site.
Rmd 9d8e5d0 Nhi Hin 2021-07-02 wflow_publish(“analysis/index.Rmd”)
html 050dcff Nhi Hin 2021-07-02 Build site.
html 76d837c Nhi Hin 2021-07-02 Build site.
Rmd ba0f166 Nhi Hin 2021-07-02 wflow_publish(“analysis/index.Rmd”)
html 8a808a2 Nhi Hin 2021-07-02 Build site.
Rmd ed2fe3c Nhi Hin 2021-07-02 wflow_publish("analysis/*.Rmd")
html 66b2c36 Nhi Hin 2021-07-02 Build site.
Rmd 9b94e39 Nhi Hin 2021-07-02 wflow_publish("analysis/*.Rmd")
html f62ae4f Nhi Hin 2021-06-30 Build site.
Rmd 38f8dca Nhi Hin 2021-06-30 wflow_git_commit(all = TRUE)
Rmd 02f3417 Nhi Hin 2021-06-29 Start workflowr project.


  1. Ensure that RStudio is installed. Install the renv package by running the following line in the RStudio Console:
  1. Download the workshop material by clicking here and unzip the folder.
  1. In the RStudio Console, run the following lines of code to download and install all required packages using renv:
renv::restore(library = "./rlib/")
.libPaths( c( .libPaths(), "./rlib") )
  1. You are ready to start running through the workshop material!

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5        whisker_0.4       knitr_1.30        magrittr_2.0.1   
 [5] R6_2.5.0          rlang_0.4.10      fansi_0.4.1       stringr_1.4.0    
 [9] tools_4.0.3       xfun_0.23         utf8_1.1.4        git2r_0.27.1     
[13] jquerylib_0.1.3   htmltools_0.5.1.1 ellipsis_0.3.1    rprojroot_2.0.2  
[17] yaml_2.2.1        digest_0.6.27     tibble_3.1.1      lifecycle_1.0.0  
[21] crayon_1.4.1      later_1.1.0.1     sass_0.3.1        vctrs_0.3.7      
[25] promises_1.1.1    fs_1.5.0          glue_1.4.2        evaluate_0.14    
[29] rmarkdown_2.8     stringi_1.5.3     bslib_0.2.4       compiler_4.0.3   
[33] pillar_1.6.0      jsonlite_1.7.2    httpuv_1.5.4      pkgconfig_2.0.3