HTSFilter

"HTSFilter" is a software tool to enhance RNA sequencing data analysis, addressing the challenge of differential expression analysis among various experimental conditions. Due to the large number of genes analyzed in these studies, there is a need to strictly control the false-discovery rate, which often comes at the cost of reducing the detection power for genuinely differentially expressed genes. A standard but ad hoc solution is to filter out genes with low signal intensity, though the impact of such filtering on downstream analysis is seldom assessed.

HTSFilter stands out with its unique, data-driven approach for determining an optimal filtering threshold. This innovative method leverages the Jaccard similarity index to selectively remove lowly expressed genes from the analysis. By adopting this approach, HTSFilter significantly boosts the detection power for moderately to highly expressed genes. A standout feature of HTSFilter is its adaptability; its data-driven threshold can vary across different experiments, showcasing its versatility and applicability to a broad spectrum of RNA sequencing studies.