Last updated: 2026-07-03

Checks: 2 0

Knit directory: immgenT-GP-analysis/analysis/

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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: 8ac7f9f

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The results in this page were generated with repository version 8ac7f9f. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
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Unstaged changes:
    Modified:   code/R/setup_data.R
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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
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.

Supplementary tables

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