Landscape of Multi-Modal Programmed Cell Death and Immune Microenvironment Remodeling in Thoracic Ossification of the Ligamentum Flavum: Integrative Bioinformatic Analysis with Epitranscriptomic and Single-Cell Validation — Analysis Code
Abstract
Analysis code accompanying the manuscript "Landscape of Multi-Modal Programmed Cell Death and Immune Microenvironment Remodeling in Thoracic Ossification of the Ligamentum Flavum: Integrative Bioinformatic Analysis with Epitranscriptomic and Single-Cell Validation" (submitted to Journal of Clinical Medicine). Contents: - 01-14: bulk transcriptome analysis scripts for GSE113212 (differential expression, GSVA/ssGSEA PCD scoring, immune infiltration, enrichment, m6A regulator analysis, LASSO signature, nomogram/DCA, figure panels). - 02b/09b/14b-14e, fix_Fig4E_title.R: post-hoc figure fixes (title clipping corrections); rerun logs are included for transparency. - sc_01c - sc_07: single-cell RNA-seq analysis of GSE294458/GSE267819 (QC, annotation, validation, cross-cohort validation, CellChat, pseudotime) and server-side scripts for GSE271018. - 07b/11a: m6A MeRIP-seq preprocessing and platform annotation. - rerun_logs_2026-10-13/, server_rerun_2026-10-13/: execution logs of the final reproduction runs. Environment: R 4.5.3; key packages limma, edgeR, GSVA, fgsea, glmnet, pROC, Seurat v5, harmony, CellChat v1.6.1, monocle3, rms, dcurves, Biostrings, ggplot2, pheatmap, and the g:Profiler web API. Random seeds are fixed where applicable (e.g., AddModuleScore seed = 42). Data: all input datasets are publicly available from the Gene Expression Omnibus (GSE113212, GSE206560, GSE106253, GSE294458, GSE267819, GSE271018); no new human or animal experiments were performed. Note on CIBERSORT: the CIBERSORT R script and LM22 signature matrix are NOT redistributed here, as their license (Newman lab, Stanford) permits non-commercial academic use only and prohibits public redistribution. Please obtain them from https://cibersortx.stanford.edu/ to reproduce the CIBERSORT-based analyses. Figure 3C schematic: created with FigDraw (www.figdraw.com), AI-assisted generation followed by manual editing; export ID IUOUU7179f.
