rnaseqdea-package: rnaseqdea: RNA-Seq Differential Expression Analysis...

In wanchanglin/rnaseqdea: RNA-Seq Differential Expression Analysis (rnaseqdea)

rnaseqdea: RNA-Seq Differential Expression Analysis (rnaseqdea)

Description

rnaseqdea provides functions for RNA-Seq differential expression analysis. It implements wrapper functions to call differential statistical models to perform analysis. This package also provides a unified normalisation methods for all used modelling methods. Some plots are implemented for these modelling.

Wrapper functions for statistical analysis methods

• DESeq2

• edgeR

• NBPSeq

• EBSeq

• NOISeq

• SAMseq

• voom+limma

• TSPM

• hypothesis testing

Normalisation methods

• Normal factor: DESeq, TMM, RLE, UQ. Use for modelling.

• Variance stabilizing transformation (VST) and Regularized log transformation (RLT) implemented in package DESeq2. Use for the classification and visualisation.

Plots

• MA plot

• Volcano plot

• Histogram of p-values

• PCA plot

• MDS plot

• Boxplot

See Also

Useful links:

• https://github.com/wanchanglin/rnaseqdea

• Report bugs at https://github.com/wanchanglin/rnaseqdea/issues

wanchanglin/rnaseqdea documentation built on June 2, 2025, 1:05 a.m.