Integrating trajectory inference and gene regulatory network analysis to resolve transcriptional programs of T cell state transitions in the tumor microenvironm... (opens in new tab)

Reconstructing dynamic immune cell state transitions from single-cell transcriptomic data requires coordinated analytical strategies that capture both phenotypic progression and underlying regulatory programs. This protocol describes a step-by-step computational workflow for analyzing human tumor-infiltrating T cells using the sequential application of dimensionality reduction, pseudotime trajectory inference, regulon activity analysis, and transcription factor-transcription factor network re...