Topconfects R package

Topconfects is an R package intended for RNA-seq or microarray differntial expression analysis, where we are interested in placing confidence bounds on many effect sizes (one per gene) from few samples. In the simplest case, the effect size of interest is log₂ fold change. Topconfects builds on TREAT p-values offered by the limma and edgeR Bioconductor packages or the "greaterAbs" test offered by DESeq2. It tries a range of effect sizes using the TREAT method, and uses this to produce a list of genes ranked by confident effect size while maintaining a given FDR.

Ongoing development of this package occurs at https://github.com/pfh/topconfects