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DESeq2(R) Analysis environment setup
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.
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)
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")