workflowr

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Last updated: 2025-09-10

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.

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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.

Repository version: e850d21

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 e850d21. 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

Untracked files:
    Untracked:  analysis/x202504.Rmd
    Untracked:  analysis/x202505.Rmd
    Untracked:  analysis/x202506.Rmd
    Untracked:  analysis/x202506_stats.Rmd
    Untracked:  analysis/x202506_tidyverse.Rmd
    Untracked:  analysis/x202507.Rmd

Unstaged changes:
    Modified:   analysis/0_resources.Rmd
    Deleted:    analysis/202504.Rmd
    Deleted:    analysis/202505.Rmd
    Deleted:    analysis/202506.Rmd
    Deleted:    analysis/202506_stats.Rmd
    Deleted:    analysis/202506_tidyverse.Rmd
    Deleted:    analysis/202507.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/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
html	bbeea56	DrThomasOneil	2025-09-10	Build site.
Rmd	14b16ea	DrThomasOneil	2025-09-10	wflow_publish(c("analysis/202509.Rmd", "analysis/202510.Rmd"))
html	377b249	DrThomasOneil	2025-09-05	Build site.
Rmd	e4e2d0c	DrThomasOneil	2025-09-05	wflow_publish(files)
html	4673160	DrThomasOneil	2025-09-04	Build site.
Rmd	3ca5193	DrThomasOneil	2025-09-04	wflow_publish("analysis/202509.Rmd")
html	6f8a683	DrThomasOneil	2025-09-04	Build site.
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)

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Getting to the bottom of intestinal diseases through genomics

Zoom link

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Wednesday 10th September (WIMR Seminar Room & Zoom)

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

Invited Speaker: Dr 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 (1pm - 3pm)

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!

Sign up below:

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