consensusDE

The software tool 'consensusDE' automates identifying significant differential expression (DE) by combining results from multiple RNA-seq algorithms. It addresses the challenge of running multiple algorithms to identify common significant differences while integrating and assessing the impact of removing unwanted variation (RUV) into all algorithms. The tool requires minimal user input, such as a table describing sample groups, a directory containing BAM files or preprocessed count tables, and an optional transcript database for annotation. It supports various analysis settings, including merging technical replicates and paired analyses, and provides a compendium of plots for user guidance. The study evaluates the impact of RUV on DE stability when combined with multiple algorithms and between algorithms using real and simulated data.