Isoform-Level Spline Modeling Approach for Longitudinal Transcriptomics

This repository contains the code and analysis pipelines for modeling longitudinal salivary transcriptome dynamics using natural splines. It supports the manuscript:

Differential Analysis Reveals Isoform Switching Following Pneumococcal Vaccination
Yeokyoung (Anne) Kil, Lior Pachter.
bioRxiv, 2025
DOI: https://doi.org/10.1101/2025.03.09.642237

This study uses spline regression to analyze longitudinal RNA-seq data and demonstrate its advantages in isoform-level differential expression analysis. Original data used for this study was published by Mias et. al., 2021. The repository includes:

• R scripts for spline model fitting & DE analysis
• Python scripts for spline visualization
• PCA visualization from sleuth outputs (Python, R)
• Processed outputs for pathway analysis and gene-level comparison
• Supplementary files for transparency and reproducibility