stageR

stageR is a software tool designed for RNA sequencing studies that involve complex designs and transcript-resolution analyses. It addresses the challenge of controlling the false discovery rate (FDR) at the gene level, which is often a problem with conventional approaches. To overcome this, stageR employs a two-stage testing paradigm that leverages the increased power of aggregated gene-level tests.

What sets stageR apart from other software tools is its ability to perform post hoc assessment for significant genes, providing gene-level FDR control and boosting power for testing interaction effects. Additionally, stageR provides a framework for transcript-level analysis that performs powerful gene-level tests while maintaining biological interpretation at transcript-level resolution.

The procedure is applicable whenever individual hypotheses can be aggregated, providing a unified framework for complex high-throughput experiments. Thus, stageR is an essential tool for researchers and scientists working in RNA sequencing, providing a powerful and effective method for analyzing complex designs and transcript-resolution analyses.