Matrix factorization analyses of the immgenT scRNA-seq data

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Last updated: 2026-07-28

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Knit directory: immgenT-GP-analysis/analysis/

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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	d538aa2	Ziang Zhang	2026-07-28	Build site: reordered Figures 6 / S6 / S3 and the new Figure 7b page
Rmd	4c07670	Ziang Zhang	2026-07-28	Reorder Figures 6, S6 and S3; make the ex-S5 figure Figure 7b
html	029b0ae	Ziang Zhang	2026-07-28	Build site.
Rmd	0f5b5da	Ziang Zhang	2026-07-28	Align all figure captions with captions_20260728_final.docx
html	d0ebed0	Ziang Zhang	2026-07-28	Build site: Extended Data Table 7 as the manual protein threshold list
Rmd	cf77f4e	Ziang Zhang	2026-07-28	Extended Data Table 7: swap GP gating alignment for the manual protein thresholds
html	3fc3789	Ziang Zhang	2026-07-27	Republish all 24 pages
html	1390a03	Ziang Zhang	2026-07-27	Republish all 24 pages
html	adaef21	Ziang Zhang	2026-07-27	Build site: panel fixes and PDF-derived assets
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

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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.

Main figures

• Figure 1: Overview of the 200 gene programs in immgenT
• Figure 2: Active genes and cells in gene programs
• Figure 3: T cell lineage-related GPs
• Figure 4: GPs associated with T cell activation
• Figure 5: GP expression in tissues is driven by T cell composition
• Figure 6: Surface proteins associated with GP activity
• Figure 7b: EBMF versus matched-RQVI factor comparison across level-2 clusters

Figure 7 (RQVI validates EBMF-derived gene programs with a non-linear deep learning framework) is otherwise produced by our collaborator’s RQVI pipeline, not by this repository; only its panel b is ours, and the page above covers that panel alone.

Extended Data figures

Published as Extended Data Figures 1-4, 6 and 7; the page names below keep the older FigureS* form so existing links stay valid. There is deliberately no Extended Data Figure 5: it became main Figure 7b on 2026-07-28 and the remaining figures kept their numbers rather than shifting up.

• Figure S1 / Extended Data Figure 1: Reproducibility across IGTs and batch-effect evaluation
• Figure S2 / Extended Data Figure 2: Tz- and CD8-specific GPs (GP30 and GP58)
• Figure S3 / Extended Data Figure 3: Characterizing activation-associated GPs
• Figure S4 / Extended Data Figure 4: Healthy non-thymocyte GP mean-loading heatmaps
• Figure S6 / Extended Data Figure 6: Protein programs, CD69-associated GPs, and further gating strategies

Extended Data Figure 7 (RQVI scalability and representative matches to lineage-associated EBMF GPs) is likewise produced by the collaborator’s RQVI pipeline and has no page here.

Extended Data tables

• Extended Data Table 1: summary of GP characteristics and annotations
• Extended Data Table 2: GP AUC by lineage
• Extended Data Table 3: GP AUC by tissue
• Extended Data Table 4: GP AUC by cluster
• Extended Data Table 5: GP activity during activation
• Extended Data Table 6: protein factor matrix
• Extended Data Table 7: protein gating (manual protein positivity thresholds)
• Extended Data Table 8: comprehensive gene signature matrix (wide format)

Methods

• Fitting EBMF using flashier
• Fitting CITE-seq protein programs with fixed scRNA loadings

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