Last updated: 2025-09-04

Checks: 2 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.


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! 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 c73a3b6. 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/
    Ignored:    todo.R

Unstaged changes:
    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/202509.Rmd) and HTML (docs/202509.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 c73a3b6 DrThomasOneil 2025-09-04 wflow_publish(files)
html 0dd27e2 DrThomasOneil 2025-08-13 Build site.
html 05dd2b2 DrThomasOneil 2025-08-12 Build site.
Rmd f7d60d2 DrThomasOneil 2025-08-12 wflow_publish(files)

September events

Zoom link


Wednesday 3rd September (WIMR C2.31 & Zoom)

Coding club (1pm - 3pm)

Bring your codes, data, and questions. Enjoy the time and space for networking, collaboration, helping each other, or focusing on coding/analysis/statistics. We would also cover the Python set-up for the workshop this month.

Wednesday 10th September (WIMR Seminar Room & Zoom)

Getting to the bottom of intestinal disease through genomics (11am - 12pm)

Invited Speaker: Prof Kylie James  

Dr Kylie James is Head of the Gut Immunogenomics Laboratory at Garvan Institute of Medical Research. Her research focuses on how environmental factors shape gut immune cell and microbial landscapes in health and diseases such as inflammatory bowel disease and colorectal cancer. To achieve this goal, Kylie applies single-cell transcriptomics and computational approaches to reconstruct cellular microenvironments, developmental hierarchies and interactions.

Single-cell analysis in python (12pm - 1pm)

Invited speaker: Dr Jacqueline Tearle 

Dr Jacqueline Tearle is a Postdoc in Kylie’s lab. During her PhD, Jac developed a novel single-cell isolation technique and applied it to study changes in gene expression during melanoma tumour escape and invasion. She has since led the characterisation of a rare inflammatory bowel disease subtype using single-cell RNA sequencing, 16S microbial amplicon sequencing, and spatial transcriptomics, and now uses these multi-omic techniques to investigate early-onset colorectal cancer.

Lunch from 12pm!

Wednesday 17th September (WIMR C2.31)

Coding club (1pm - 3pm)

Bring your codes, data, and questions. Enjoy the time and space for networking, collaboration, helping each other, or focusing on coding/analysis/statistics.

Wednesday 24th September (WIMR C2.31)

Data Insight Forum (1pm - 3pm)

Connect directly as a community of analysts, present your work and get feedback from others. The general structure will be round-table updates and 5-minute presentations on real-world data analysis questions.

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