GitHub - BioinfoUSAL/Rvisdiff: Creates interactive graphs with 'R' for most popular differential expression methods (original) (raw)

Rvisdiff

Rvisdiff is an R/Bioconductor package which generates an interactive interface for the interpretation of differential analysis tests results. It generates a local Web page which enables the exploration of statistical analysis results with the generation of auto-analytical visualizations. The package supports as input the output of popular differential expression packages such as DESeq2, EdgeR and limma.

Install

installing from bioconductor

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rvisdiff")

installing from github

library(devtools) install_github('BioinfoUSAL/Rvisdiff')

Usage

Load example data

library("airway") data("airway") se <- airway se$dex <- relevel(se$dex, ref="untrt") countdata <- assay(se)

Differential expression analysis

library("DESeq2") dds <- DESeqDataSet(se, design = ~ cell + dex) dds <- DESeq(dds) dr <- results(dds, independentFiltering = FALSE)

Rvisdiff report generation

library("Rvisdiff") DEreport(dr, countdata, se$dex)