rnaseqcomp: A benchmark for RNA-seq quantification pipelines

Introduction

RNA sequencing (RNA-seq) has been utilized as the standard technology for measuring the expression abundance of genes, transcripts, exons or splicing junctions. Numerous quantification methods were proposed to quantify such abundances with/without combination of RNA-seq read aligners. It is currently difficult to evaluate the performance of the best method, due in part to the high costs of running assessment experiments as well as the computational requirements of running these algorithms. rnaseqcomp package provides a series of statistical summaries and data visualization techniques to evaluate the performance of these metohods.

Installation

rnaseqcomp is an R/bioconductor package, which can be installed with source code documented in GitHub or through Bioconductor.

Install rnaseqcomp through GitHub with following code.

library(devtools)
install_github("tengmx/rnaseqcomp")

Or, install through Bioconductor as follows.

source("https://bioconductor.org/biocLite.R")
biocLite("rnaseqcomp")

Using rnaseqcomp

First, load the package into R.

library(rnaseqcomp)

Details of how to use this package, please see the vignette.

Help

You are very welcome to leave any questions/bug messages at GitHub issues.