DESeq2R Analysis

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Contents

DESeq2(R) Analysis environment setup

Overview

With OmicSoft Suite v11.3, you can run the R implementation of DEseq2 directly from OmicSoft Studio, right from the OmicSoft Studio GUI. Because of significant improvements of DEseq2 over the past several years, OmicSoft recommends using the R implementation instead of the native OmicSoft Suite implementation of DEseq2.

This page describes the steps to install and configure R and DEseq2 for execution by OmicSoft Suite.

Installing dependencies

To run DEseq2(R), you will need to install DEseq2 in the appropriate environment; if properly installed, OmicSoft Suite will be able to call your R installation to automatically submit your data for analysis and import full results into your OmicSoft Studio project.

1. Install the R environment on your local computer or OmicSoft Server; R version 4.0 is strongly recommended for DEseq2

2. Install the Bioconductor version compatible with your R version

3. Install the DEseq2 package

Windows Installation: R 4.0.4

Not required if you will run DEseq2 remotely on your Linux-based OmicSoft Server.

Required if you plan to run DEseq2 on your local Windows machine, or are running OmicSoft Server on a Windows Server.

Download R from https://cran.r-project.org/bin/windows/base/ and follow the executor's steps.

Then be sure to update OmicSoft Studio's SetLocalRScriptEngine.pdf.

Linux Installation R 4.0.4

curl -O https://cran.r-project.org/src/base/R-4/R-4.0.4.tar.gz
tar zxvf R-4.0.4.tar.gz; cd R-4.0.4/
./configure --enable-R-shlib; make; sudo make install

R --version
R version 4.0.4 (2021-02-15) -- "Lost Library Book"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

Install DESeq2

Run each step below in the R environment to install DEseq2:

#Enter the R environment
R
# update Bioconductor Manager to the latest version
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.13")
# install deseq2
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")