Last updated: 2026-07-05

Checks: 1 1

Knit directory: immgenT-GP-analysis/analysis/

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R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Repository version: 6d1c6c0

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 6d1c6c0. 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:    .claude/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/assets/.DS_Store
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Untracked files:
    Untracked:  analysis/ExtendedDataTable1.Rmd
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    Untracked:  figures/generated/ExtendedDataTable1_GP_summary.csv
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    Untracked:  tables/

Unstaged changes:
    Deleted:    analysis/TableS1.Rmd
    Modified:   analysis/index.Rmd
    Modified:   code/R/gated_protein_helpers.R
    Modified:   code/R/roc_auc.R
    Modified:   code/README.md
    Modified:   code/pipeline/02_compute_auc.R
    Deleted:    figures/generated/Supplementary_Table1_GP_summary.csv
    Modified:   script/README.md
    Deleted:    script/TableS1.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/index.Rmd) and HTML (docs/index.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 92021bf Ziang Zhang 2026-07-03 Build site.
html 827c89b Ziang Zhang 2026-07-03 Build site.
Rmd f9db962 Ziang Zhang 2026-07-02 Simplify layout: drop old code/script folders, rename
html c6e5086 Ziang Zhang 2026-07-02 Build site.
html 5a79883 Ziang Zhang 2026-07-02 Build site.
Rmd 2b0e445 Ziang Zhang 2026-07-02 Fix GitHub source links to point at the new
html cf1d0ac Ziang Zhang 2026-07-02 Build site.
Rmd 06b2461 Ziang Zhang 2026-07-02 Initial commit: immgenT-GP-analysis
html 06b2461 Ziang Zhang 2026-07-02 Initial commit: immgenT-GP-analysis

This site documents the gene program (GP) factorization analysis of the ImmGen-T single-cell RNA-seq/CITE-seq data: ~200 GPs learned by empirical Bayes matrix factorization (EBMF), and how they relate to cell lineage, tissue, activation state, transcription factors, and surface protein expression.

Each page below covers one published figure: for every panel, the R code that produced it, the figure itself, and a short caption explaining what it shows.

Reproducing these figures

Every page above is generated by a single R script in script/, which sources shared plotting/data-loading helpers from code/R/. To regenerate a figure yourself, run (from the repository root):

Rscript script/Figure1.R