Topconfects

The software tool "Topconfects" addresses the challenge of effectively ranking genes in the context of differential gene expression analysis, especially when the gene set is large and cumbersome to investigate thoroughly. Traditional methods often rely on p values, which may have limitations. Instead, Topconfects proposes a ranking approach based on confidence bounds on the log fold change, leveraging the TREAT test.
Topconfects introduces confidence bounds that offer guaranteed control over false discovery and coverage-statement rates. By applying this method to a breast cancer dataset, Topconfects identifies top-ranked genes that emphasize distinct biological processes compared to those identified by p values.