Bioconductor Code: Rvisdiff (original) (raw)

# Rvisdiff Rvisdiff is an R/Bioconductor package which generates an interactive interface for the interpretation of differential expression 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 ```r # installing from bioconductor if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rvisdiff") # installing from github library(devtools) install_github('BioinfoUSAL/Rvisdiff') ``` # Usage ```r # 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) ```