Last updated: 2024-09-19

Checks: 2 0

Knit directory: spatialsnippets/

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.

Repository version: 511594f

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 511594f. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/e_neighbourcellchanges.nb.html
    Ignored:    analysis/glossary.nb.html
    Ignored:    renv/library/
    Ignored:    renv/staging/

Unstaged changes:
    Modified:   .gitignore

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/index_data.Rmd) and HTML (docs/index_data.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 511594f swbioinf 2024-09-19 wflow_publish("analysis/")
html 5347093 swbioinf 2024-09-17 Build site.
Rmd 7eec547 swbioinf 2024-09-17 wflow_publish("analysis/")
html 2e26929 Sarah Williams 2024-03-25 Build site.
Rmd 0a3a1ae Sarah Williams 2024-03-25 wflow_publish("analysis/")
html 30da140 Sarah Williams 2024-03-22 Build site.
Rmd 89c3371 Sarah Williams 2024-03-22 wflow_publish(c("analysis/index_data.Rmd", "analysis/index.Rmd",
html bd24df4 Sarah Williams 2023-11-01 Build site.
Rmd 8b1c005 Sarah Williams 2023-11-01 wflow_publish("analysis")
html e7a4c12 Sarah Williams 2023-10-18 Build site.
Rmd 507ead4 Sarah Williams 2023-10-18 wflow_publish("analysis/")

Source of data.

These examples assume that the data has been loaded, preprocessed (e.g. QC-ed, UMAP) and annotated (e.g. sample names, cell types, cell niches). For information, the preprocessing applied here is included in data preparation below. Please note that these are not full annotations, and do not aim to reproduce the authors’ published analyses! These are much simplified simply as a way to run these tests.