Matrix factorization analyses of the immgenT scRNA-seq data

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Last updated: 2026-07-08

Checks: 1 1

Knit directory: immgenT-GP-analysis/analysis/

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Repository version: 82e9068

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    Modified:   script/README.md

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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	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	2026-07-03	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

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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
• Figure 2: GPs and lineages
• Figure 3: GPs associated with T-cell activation
• Figure 4: GPs and tissue
• Figure 6: Linking GPs to proteins

Supplementary figures

• Figure S1: GP reproducibility across IGTs
• Figure S2: GP30 and GP58 loadings across T-cell subsets
• Figure S3: Characterizing activation GPs
• Figure S6: GP loadings recover protein-gated populations across GPs

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 during activation
• Extended Data Table 6: protein factor matrix
• Extended Data Table 7: protein gating
• Extended Data Table 8: comprehensive gene signature matrix (wide format)

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