workflowr

• Summary
• Checks
• Past versions

Last updated: 2025-05-23

Checks: 7 0

Knit directory: DigitalResearchSkillsNetwork/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

---

R Markdown file: up-to-date

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.

Environment: empty

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.

Seed: set.seed(1337)

The command set.seed(1337) 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.

Session information: recorded

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

Cache: none

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

File paths: relative

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

Repository version: 15d20dd

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 15d20dd. 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:    analysis/.DS_Store
    Ignored:    analysis/.RData
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/adit/.DS_Store
    Ignored:    plots/
    Ignored:    raw/

Untracked files:
    Untracked:  analysis/x202504_InFocus.Rmd
    Untracked:  analysis/x202504_Seminar.Rmd
    Untracked:  analysis/x202504_Workshop.Rmd
    Untracked:  analysis/x202505_InFocus.Rmd
    Untracked:  analysis/x202505_Seminar.Rmd
    Untracked:  analysis/x202505_Workshop.Rmd

Unstaged changes:
    Deleted:    analysis/202504_InFocus.Rmd
    Deleted:    analysis/202504_Seminar.Rmd
    Deleted:    analysis/202504_Workshop.Rmd
    Deleted:    analysis/202505_InFocus.Rmd
    Deleted:    analysis/202505_Seminar.Rmd
    Deleted:    analysis/202505_Workshop.Rmd
    Deleted:    analysis/adit/0_content management.csv
    Modified:   workflow.R

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/0_contacts_committee.Rmd) and HTML (docs/0_contacts_committee.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
html	e794405	DrThomasOneil	2025-05-15	Build site.
html	fb553e5	DrThomasOneil	2025-05-14	Build site.
html	cff7923	DrThomasOneil	2025-05-07	Build site.
html	16a9613	DrThomasOneil	2025-04-30	Build site.
html	862d6b6	DrThomasOneil	2025-04-29	Build site.
Rmd	b68287f	DrThomasOneil	2025-04-29	wflow_publish(files)

---

Digital Research Skills Network
Committee Members

Committee Chair Thomas O’Neil PostDoc thomas.oneil@sydney.edu.au I have been with the Mucosal Immunity lab at WIMR since my honours year in 2018. I completed my PhD in 2023. Initially, my studies involved characterising anogenital T cells by flow cytometry, but having learned analytic programming during COVID, I now study all aspects of human tissue immunology via high-parameter proteomic and transcriptomic bioinformatic approaches.	Secretary Harry Robertson PhD Candidate harry.robertson@sydney.edu.au I am a research student and aspiring bioinformatician at WIMR who was recently awarded a Fulbright Future Scholarship (Postgraduate) hosted by Harvard University. my reent focus has been on identifying biomarkers for organ transplant health using advanced imaging techniques. My approach leverages machine learning to analyse imaging data, aiming to develop a universally available, non-invasive diagnostic tool for transplant recipients.	Communications Lead Nicole Fewings PostDoc Bio
Communications Deputy Elizabeth Dunn PhD Candidate Bio	Events Coordinator Sifan Zhang PhD Candidate sifan.zhang@sydney.edu.au I am currently a PhD candidate in vaccine adjuvant group in WIMR. I have previous experience in scRNA sequencing and high-parameter flow cytometry, and I am investigating adjuvant modes of action using spatial transcriptomics (Xenium).	Content Coordinator Yuchen Li PhD Candidate yuli0321@uni.sydney.edu.au I am a PhD candidate at WIMR. Following on from Honours, my research focus is characterising human anogenital tissue CD4 T cells and their susceptibility to HIV. I aim to determine the initial establishment of HIV latency within anogenital tissues using both wet-lab experimental models and verification, and machine learning-aid computational analysis.
Level 2 Representative Suat Dervish Core Facilities Bio	Level 3 Representative Vacant Vacant Bio	Level 4 Representative Vacant Vacant Bio
Level 5 Representative Jennifer Li Group Leader jennifer.li@wimr.org.au I am a Nephrologist and Transplant Physician at Westmead hospital and researcher in the Transplant Genomics Group at WIMR.	Level 6 Representative Artur Shvetcov Senior Bioinformatician Bio	Level 7 Representative Ellis Patrick Group Leader Bio
External Representative Erin Coll PhD Candidate Bio	External Representative Shreya Rajesh Rao PhD Candidate Bio	External Representative Givanna Putri PostDoc Bio

Session information

sessionInfo()

R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.3

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Australia/Brisbane
tzcode source: internal

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

other attached packages:
[1] readr_2.1.5     dplyr_1.1.4     workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] bit_4.6.0         jsonlite_1.9.1    crayon_1.5.3      compiler_4.4.0   
 [5] promises_1.3.2    tidyselect_1.2.1  Rcpp_1.0.14       stringr_1.5.1    
 [9] git2r_0.35.0      parallel_4.4.0    callr_3.7.6       later_1.4.1      
[13] jquerylib_0.1.4   yaml_2.3.10       fastmap_1.2.0     R6_2.6.1         
[17] generics_0.1.3    knitr_1.50        tibble_3.2.1      rprojroot_2.0.4  
[21] tzdb_0.5.0        bslib_0.9.0       pillar_1.10.1     rlang_1.1.6      
[25] cachem_1.1.0      stringi_1.8.4     httpuv_1.6.15     xfun_0.51        
[29] getPass_0.2-4     fs_1.6.5          sass_0.4.9        bit64_4.6.0-1    
[33] cli_3.6.4         magrittr_2.0.3    ps_1.9.0          digest_0.6.37    
[37] processx_3.8.6    vroom_1.6.5       rstudioapi_0.17.1 hms_1.1.3        
[41] lifecycle_1.0.4   vctrs_0.6.5       evaluate_1.0.3    glue_1.8.0       
[45] whisker_0.4.1     rmarkdown_2.29    httr_1.4.7        tools_4.4.0      
[49] pkgconfig_2.0.3   htmltools_0.5.8.1

Digital Research Skills Network
Contact us