Transcriptomic analysis is fundamental to understanding gene expression dynamics across biological processes, disease mechanisms, and therapeutic development. However, rapid technological evolution (e.g., single-cell, spatial, long-read sequencing) and fragmented analytical pipelines challenge reproducibility and cross-study comparison, hindering scientific progress.

This Methods Collection aims to curate authoritative, standardized protocols and analytical workflows for the full transcriptomics lifecycle—from experimental design and library preparation to computational analysis and interpretation. Each method will be rigorously validated, benchmarked, and include open-source code/parameters.

This collection supports the research community in the following ways:

Improving reproducibility through carefully vetted, step-by-step guidelines that reduce technical variability
Accelerating the adoption of emerging technologies, such as spatial transcriptomics, by making best practices readily accessible.
Fostering collaboration through standardized outputs that allow for smooth data integration and meta-analyses.
Minimizing resource waste by addressing inefficiencies in experimental pipeline development.

Kezhong Zhang