cqn

The "cqn" software tool addresses a critical challenge in molecular biology: the unwanted variability in gene expression data derived from genome-wide assays, including microarrays and RNA sequencing (RNA-seq) technologies. Despite initial excitement over RNA-seq's potential for reduced variability compared to microarrays, cqn highlights that RNA-seq data exhibit sample-specific variability, notably influenced by guanine-cytosine (GC) content. This variability, if not corrected, can lead to false positives in downstream analyses, undermining the reliability of the data.