Last updated: 2026-07-27

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Knit directory: immgenT-GP-analysis/analysis/

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R Markdown file: up-to-date

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Repository version: ea3ecc2

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Ignored files:
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    Ignored:    analysis/.DS_Store
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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
html 5b19858 Ziang Zhang 2026-07-27 Build site.
html 9862b6d Ziang Zhang 2026-07-23 Build site.
Rmd 98d2924 Ziang Zhang 2026-07-23 Reword Figure S5 page for a publication audience
html 9398c72 Ziang Zhang 2026-07-23 Publish Figure S5 workflowr page
Rmd b9f4f58 Ziang Zhang 2026-07-23 Add Figure S5: EBMF vs matched-RQVI level2-cluster comparison
Rmd b197499 Ziang Zhang 2026-07-16 Restructure main figures (renumber + split Figure 1)
html b197499 Ziang Zhang 2026-07-16 Restructure main figures (renumber + split Figure 1)
Rmd f0c481d Ziang Zhang 2026-07-14 Document CITE-seq fixed-loading EBMF workflow
html f0c481d Ziang Zhang 2026-07-14 Document CITE-seq fixed-loading EBMF workflow
Rmd c344aaa Ziang Zhang 2026-07-13 Add Figure S4 mean-loading heatmaps
html c344aaa Ziang Zhang 2026-07-13 Add Figure S4 mean-loading heatmaps
Rmd cba8dd4 Ziang Zhang 2026-07-12 Add Methods page: Flashier matrix factorization
html cba8dd4 Ziang Zhang 2026-07-12 Add Methods page: Flashier matrix factorization
html c5cbc77 Ziang Zhang 2026-07-08 Build site.
Rmd fb8c855 Ziang Zhang 2026-07-08 Add Extended Data Table 8: comprehensive gene signature matrix (long + wide)
html 92d1365 Ziang Zhang 2026-07-05 Build site.
Rmd d07f797 Ziang Zhang 2026-07-05 Replace Table S1/S2/S3 with 7 fully-reproducible Extended Data Tables
html 92021bf Ziang Zhang 2026-07-02 Build site.
html 827c89b Ziang Zhang 2026-07-02 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