README.md

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

The rnaseqdea R package

Overview

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.

Visualisation

• MA plot
• Volcano plot
• Histogram of p-values
• PCA plot
• MDS plot
• Boxplot

Installation from GitHub

This package is only in GitHub. To install, use:

devtools::install_github("wanchanglin/rnaseqdea")

Or install with vignette:

devtools::install_github('wanchanglin/rnaseqdea', build_vignettes = TRUE)
browseVignettes("rnaseqdea")

Usage

See the help pages of the package for details.

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