workflowr

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• Checks
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Last updated: 2025-05-15

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: b102ce1

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 b102ce1. 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/adit/0_content management.csv
    Untracked:  analysis/x202504_Workshop.Rmd

Unstaged changes:
    Deleted:    analysis/202504_Workshop.Rmd
    Modified:   analysis/_site.yml
    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/202505_InFocus.Rmd) and HTML (docs/202505_InFocus.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	fb553e5	DrThomasOneil	2025-05-14	Build site.
Rmd	a5f07d7	DrThomasOneil	2025-05-14	wflow_publish(files)
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)
Rmd	2b35382	DrThomasOneil	2025-04-26	upd

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Spatial Transcriptomics:

Experimental Considerations and Analysis by 10X Genomics

In this session, 10X Genomics will lead the discussion on the key analytical considerations of Visium and Xenium analysis, such as cell segmentation and panel design.

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Monday 5th May, 1 pm

WIMR Seminar Room

Zoom Link

Speakers: Geoffrey McDermott (10X Genomics)

Agenda:

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• 1-1:45: Xenium (Panel design, Cell Segmentation, Data Analysis Options and new products/proteomics)
  
• 1:45-2:15: Afternoon tea
  
• 2:15-2:45: Visium HD (Data analysis options, new products - nuclei/cell segmentation + Visium HD 3’)
  
• 2:45-3:30: Loupe and Xenium Explorer & Question Time
  

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Digital Research Skills Network
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