aFold

The software tool "aFold" addresses challenges in RNA-Seq analysis, focusing on data normalization and identifying significant differential expressions in real-life, noisy datasets. Existing tools often rely on assumptions not met by real data, such as the symmetrical distribution of up-and-down-regulated genes and a few differentially expressed genes or outliers. Additionally, arbitrary choices for selecting significant differentially expressed genes can impact downstream analysis.
aFold introduces a novel normalization procedure called qtotal, which considers the overall distribution of read counts for data standardization, enhancing the identification of differential gene expression, especially in cases of asymmetrical distributions. The tool employs a polynomial algorithm to model the uncertainty of read counts across treatments and genes.