bio-differential-expression-timeseries-de

Approaches

Method	Best For
limma with splines	Smooth temporal patterns
maSigPro	Multiple time points, regression
ImpulseDE2	Impulse-like patterns
DESeq2 LRT	Discrete time comparisons

limma with Splines

Goal: Identify genes with smooth temporal expression patterns using flexible spline models.

Approach: Fit voom-transformed counts with natural spline basis functions in limma, testing spline coefficients for significance.

"Find genes that change over time in my RNA-seq experiment" → Model temporal expression using spline regression and test whether spline terms are significantly non-zero.

Setup

library(limma)
library(edgeR)
library(splines)