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Tool: The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

# Install Bioconductor packages
BiocManager::install('DESeq2')
BiocManager::install("apeglm")
BiocManager::install("EnhancedVolcano")
BiocManager::install("Glimma")
BiocManager::install("ggrepel")
BiocManager::install('limma')
BiocManager::install('edgeR')
BiocManager::install("reactome.db")
BiocManager::install("AnnotationDbi")

# Install CRAN packages
install.packages('tidyverse')
install.packages('ggplot2')
install.packages("pheatmap")
r rnaseq installation deseq2
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written by Aditya naman • Aditya naman

Hi, appreciate the contribution but please understand that generally with "Tools" or "Tutorials" some context is required. The command to install DESeq2 is BiocManager::install('DESeq2') while all other packages are optional for downstream analysis and visualization.

• 0 views • link
written by ATpoint ATpoint

Thanks for the correction. I should also mention the downstream analysis.

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written by Aditya naman • Aditya naman

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