compcodeR--an R package for benchmarking differential expression methods for RNA-seq data.

Abstract

compcodeR is an R package for benchmarking of differential expression analysis methods, in particular, methods developed for analyzing RNA-seq data. The package provides functionality for simulating realistic RNA-seq count datasets, an interface to several of the most commonly used differential expression analysis methods and extensive functionality for evaluating and comparing different approaches on real and simulated data. compcodeR is available from http://www.bioconductor.org/packages/release/bioc/html/compcodeR.html.