sartools_deseq2

sartools_deseq2 performs differential gene expression analysis of RNA-Seq count data using the DESeq2 statistical framework, providing systematic quality control, normalization, dispersion estimation, and hypothesis testing across biological conditions.

Key Features:

• Systematic Quality Control: Implements quality control checks throughout the analysis pipeline to identify issues in RNA-Seq data.
• Normalization and Dispersion Estimation: Uses DESeq2 normalization methods and dispersion estimation for accurate modeling of count data.
• Differential Expression Testing: Performs statistical testing for differential expression across two or more conditions.
• Complex Design Handling: Supports complex experimental designs and accounts for confounders such as batch effects and sample pairings.
• Reporting: Produces HTML reports that include diagnostic plots and summaries of the analysis.
• Reproducibility: Records analysis parameters and R package versions to support reproducible research.

Scientific Applications:

• Differential expression studies: Comparative analysis of gene expression from RNA-Seq across biological conditions such as treatments or genetic variations.
• Multi-factor experimental analyses: Analysis of experiments involving multiple factors, confounders, or paired samples.

Methodology:

Systematic quality control, DESeq2-based normalization and dispersion estimation, and differential expression testing with diagnostic plots.