A comprehensive R package for RNA-seq data analysis using DESeq2. This package provides a streamlined workflow for quality control, differential expression analysis, and gene set enrichment analysis.
Main Functions
run_deseq2_pip()Main pipeline function that runs the complete analysis workflow
run_diffexp()Performs differential expression analysis between two groups
run_gsea()Performs gene set enrichment analysis
plot_volcano()Creates volcano plots for differential expression results
plot_gene_expression()Visualizes gene expression patterns
Quality Control Functions
remove_xy_genes()Removes genes on X and Y chromosomes
remove_mt_genes()Removes mitochondrial genes
remove_low_expression()Filters out lowly expressed genes
check_library()Generates library size distribution plots
run_pca()Performs principal component analysis
run_distance()Calculates and visualizes sample distances
Data Formatting Functions
import_nfcore_dds()Imports DESeq2 object from nfcore pipeline
import_msigdb()Imports MSigDB gene sets
summarize_genes()Aggregates isoform-level expression to gene-level
format_enrichmentmap()Formats results for EnrichmentMap visualization