DEWE: Differential Expression Workflow Executor

DEWE: Differential Expression Workflow Executor executes pre-configured workflows to perform differential expression analysis of RNA-seq data, identifying and quantifying differentially expressed genes and transcripts.

Key Features:

• Pre-configured workflows: Provides two established workflows covering alignment/quantification and differential expression analysis.
• Alignment and quantification: Aligns RNA-seq reads using HISAT2 or Bowtie2 and estimates transcript abundance with StringTie.
• Differential expression testing: Performs statistical testing and differential expression analysis using Ballgown and edgeR.
• Docker integration: Uses Docker for environment and dependency management to ensure reproducible execution.
• Result outputs and visualization: Generates tab-delimited result tables and figures for reporting and visualization of differential expression outputs.
• Pathway enrichment support: Produces outputs compatible with pathway enrichment and downstream post-processing workflows.

Scientific Applications:

• Transcriptomic profiling across experimental conditions: Identifies differential expression patterns in RNA-seq datasets across experimental conditions.
• Differentiation process analysis: Profiles gene expression changes during cellular differentiation processes.
• Disease state analysis: Profiles gene expression alterations associated with disease states.
• Functional and pathway inference: Supports deriving insights into cellular functions and underlying molecular mechanisms from differential expression results.

Methodology:

Align RNA-seq reads with HISAT2 or Bowtie2, estimate transcript abundance with StringTie, and identify differentially expressed genes/transcripts using Ballgown and/or edgeR.