goseq

"GOseq" is a specialized software tool designed to perform Gene Ontology (GO) analysis tailored explicitly for RNA-seq data. While crucial for simplifying complex data sets and identifying underlying biological processes in genome-wide expression studies, traditional GO analysis methods often produce biased results when applied to RNA-seq data. This bias is mainly due to the over-detection of differential expression among long and highly expressed transcripts. GOseq addresses this issue by implementing an analysis approach that corrects for these biases, ensuring more accurate and biologically relevant GO analysis outcomes. When applied to a prostate cancer dataset, GOseq significantly altered the analysis results, identifying GO categories that align more closely with the established biology of the condition, demonstrating GOseq's utility in providing a more accurate interpretation of RNA-seq data. It is a valuable tool for researchers to uncover the biological significance behind gene expression patterns.