Quality Control for RNA-Seq Data

Functions for semi-automated quality control of bulk RNA-seq data.

RNAseqQC

The goal of RNAseqQC is to aid quality control of RNAseq data by providing a collection of data visualization functions. It allows identification of samples with unwanted biological or technical effects and to explore differential testing results.

Installation

You can install the released version of RNAseqQC from CRAN with:

install.packages("RNAseqQC")

Example

This is a basic example in which we make a library complexity plot and then compare some samples to the median reference of their respective group:

library(RNAseqQC)
library("DESeq2")

dds <- makeExampleDESeqDataSet(n=10000, m=30)
plot_library_complexity(dds)
vsd <- vst(dds)
dds$condition
plot_sample_MAs(vsd, group = "condition")[c(1,2,16,17)]