workflowr

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Last updated: 2025-04-22

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.

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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: 3400f97

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 3400f97. 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/.Rhistory
    Ignored:    analysis/adit/.DS_Store

Untracked files:
    Untracked:  analysis/0_content management.csv
    Untracked:  analysis/202505.Rmd
    Untracked:  analysis/202505_InFocus.Rmd
    Untracked:  analysis/202505_Seminar.Rmd
    Untracked:  analysis/adit/head_index.html

Unstaged changes:
    Modified:   analysis/202504_Workshop.Rmd
    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.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/0_contacts.Rmd) and HTML (docs/0_contacts.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	3400f97	DrThomasOneil	2025-04-22	wflow_publish("analysis/0_contacts.Rmd")
html	938818e	DrThomasOneil	2025-04-14	Build site.
html	ed690e6	DrThomasOneil	2025-04-14	Build site.
html	cb886ef	DrThomasOneil	2025-04-10	Build site.
html	f6c0433	YuchenLi	2025-04-09	Build site.
html	8d78b0f	YuchenLi	2025-04-09	Build site.
html	7421f69	DrThomasOneil	2025-04-08	Build site.
Rmd	155c73a	DrThomasOneil	2025-04-08	wflow_publish("analysis/*.Rmd")
html	f2d3385	DrThomasOneil	2025-03-24	update
html	517dcf9	DrThomasOneil	2025-03-24	Build site.
html	6a4432b	DrThomasOneil	2025-03-24	Build site.
html	1f218f3	DrThomasOneil	2025-03-24	Build site.
html	dca90e9	DrThomasOneil	2025-03-24	Build site.
html	1d1c076	DrThomasOneil	2025-03-24	Build site.
html	956ba9b	DrThomasOneil	2025-03-24	Build site.
Rmd	6b72e34	DrThomasOneil	2025-03-24	wflow_publish(c("analysis/*.Rmd"))
html	5b8d69e	DrThomasOneil	2025-03-18	Build site.
html	d600337	DrThomasOneil	2025-03-18	Build site.
Rmd	0e68f67	DrThomasOneil	2025-03-18	wflow_publish(c("analysis/*.Rmd"))
html	b537f69	DrThomasOneil	2025-03-18	Build site.
html	b7982e9	DrThomasOneil	2025-03-16	Build site.
html	fc5dd81	DrThomasOneil	2025-03-16	Build site.
html	8e1c1a3	DrThomasOneil	2025-03-16	Build site.
html	36dc5fc	DrThomasOneil	2025-03-03	Build site.
html	49bb28c	DrThomasOneil	2025-03-03	Build site.
Rmd	97303a5	DrThomasOneil	2025-03-03	wflow_publish(c("analysis/*.Rmd"))
html	8258922	DrThomasOneil	2025-03-03	Build site.
html	71646a5	DrThomasOneil	2025-02-27	Build site.
Rmd	c05aafe	DrThomasOneil	2025-02-27	wflow_publish(c("analysis/*.Rmd"))
html	c7f5738	DrThomasOneil	2025-02-24	Build site.
html	79d09b1	DrThomasOneil	2025-02-24	Build site.
html	a5c9f2c	DrThomasOneil	2025-02-24	Build site.
html	ca2c086	DrThomasOneil	2025-02-24	Build site.
html	fca0503	DrThomasOneil	2025-02-24	Build site.
html	af42fba	DrThomasOneil	2025-02-24	Build site.
html	1aeefc7	DrThomasOneil	2025-02-20	Build site.
html	5fe30de	DrThomasOneil	2025-02-20	Build site.
html	5ef4f12	DrThomasOneil	2025-02-11	Build site.
html	f48f4f0	DrThomasOneil	2025-02-10	Build site.
html	3bfe847	DrThomasOneil	2025-02-10	Build site.
html	b14f3b5	DrThomasOneil	2025-02-10	Build site.
html	bfba3e0	DrThomasOneil	2025-02-07	Build site.
html	f3d6f87	DrThomasOneil	2025-02-04	Build site.
Rmd	525ffe6	DrThomasOneil	2025-02-04	wflow_publish(c("analysis/*.Rmd"))
html	f654b8d	DrThomasOneil	2025-02-04	Build site.
Rmd	e6ea78d	DrThomasOneil	2025-02-04	wflow_publish(c("analysis/*.Rmd"))
html	4968925	DrThomasOneil	2025-01-30	Build site.
html	299ff3d	DrThomasOneil	2025-01-28	Build site.
Rmd	272b312	DrThomasOneil	2025-01-28	wflow_publish(c("analysis/*"))
html	023005d	DrThomasOneil	2025-01-07	Build site.
Rmd	0ecb65d	DrThomasOneil	2025-01-07	Updated Getting Started in R. Chapter 1 completed
html	c893d70	DrThomasOneil	2025-01-06	Build site.
Rmd	8eec2ce	DrThomasOneil	2025-01-06	Initial Deployment
html	660b0f8	DrThomasOneil	2025-01-06	Build site.
Rmd	7cb1531	DrThomasOneil	2025-01-06	Initial Deployment
html	2e79a1d	DrThomasOneil	2025-01-06	Build site.
Rmd	451a21f	DrThomasOneil	2025-01-06	Initial Deployment

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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

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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/Sydney
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

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