zdq_deg

A Deseq2 R script for DEG analysis

Quick Start

1. -STEP01: -INSTALL Dependencies: (OR RUN THIS SCRIPTS WITH A DOCKER IMAGES)

   if (!requireNamespace("BiocManager", quietly = TRUE))
   install.packages("BiocManager")
   BiocManager::install("DESeq2")
   BiocManager::install("BiocParallel")
   BiocManager::install("optparse")
   BiocManager::install("ggplot2")
   BiocManager::install("RColorBrewer")
   BiocManager::install("pheatmap")
   BiocManager::install("dplyr")
   BiocManager::install("ggrepel")
   BiocManager::install("clusterProfiler")
   BiocManager::install("amap")
   BiocManager::install("AnnotationHub")
   BiocManager::install("org.Hs.eg.db")

2. -STEP02_Usage:( YOU CAN RUN FOLLOW SCRIPTS TO RUN A TEST pipeline )

   Rscript deseq.r \
   --count_file ./test_data/reads.txt \
   --coldata_file ./test_data/coldata.txt \
   --sample_con "tumor-normal" \
   --outprefix "zdq_deseq2"