ARMOR

ARMOR performs end-to-end processing and statistical analysis of RNA-seq data, producing quality-assessed, aligned and quantified reads, differential expression results, geneset analyses, and Bioconductor-ready objects.

Key Features:

• End-to-End Workflow: Processes RNA-seq data from initial raw read files through quality assessment, alignment, quantification, differential expression testing, geneset analysis, and outputs suitable for browser-based exploration.
• Modularity and Flexibility: Implements a modular architecture with a curated set of tools while allowing substitution of pipeline components.
• Reproducibility and Transparency: Built on the Snakemake workflow management system and uses conda environments to ensure consistent, reproducible computational environments.
• Bioconductor Integration: Generates Bioconductor objects to facilitate downstream analysis with R and Bioconductor packages.

Scientific Applications:

• Differential Gene Expression: Supports identification and statistical testing of genes with significant expression changes between conditions.
• Geneset and Pathway Analysis: Enables geneset analysis and pathway enrichment investigations to explore gene function and biological pathways.

Methodology:

Implemented as a Snakemake workflow that defines analyses as code and manages dependencies via conda environments; produces Bioconductor objects as analysis outputs.