ARPIR

ARPIR automates RNA-Seq data processing and analysis by integrating quality control, pre-processing, alignment, transcript quantification, differential expression, and tertiary analyses to support interpretation of coding and non-coding RNA expression and pathway-level insights.

Key Features:

• Automated Workflow: Integrates quality control, pre-processing, alignment, transcript quantification, and differential expression into a single automated pipeline.
• Tool Defaults and Customization: Defaults to HISAT2 for alignment, featureCounts for quantification, and edgeR for differential expression while allowing alternative tool selection, with choices evaluated for speed, RAM usage, sensitivity, and specificity.
• Supported Data Types and Designs: Handles paired-end and single-end RNA-Seq data and supports multiple treatment groups with multiple comparisons in a single run.
• Tertiary Analyses: Provides Gene Ontology (GO) and pathway analysis for downstream biological interpretation.

Scientific Applications:

• Coding and non-coding RNA profiling: Enables analysis of expression for both coding and non-coding RNAs from RNA-Seq datasets.
• Comparative transcriptomics: Supports differential expression and multiple-group comparisons across treatment conditions.
• Disease mechanism and biomarker studies: Facilitates identification of differentially expressed genes and pathway-level changes relevant to disease mechanisms and biomarker discovery.
• Regulatory RNA analysis: Supports investigation of regulatory RNA elements through expression and downstream functional analyses.

Methodology:

Performs quality control and pre-processing, alignment (HISAT2), transcript quantification (featureCounts), differential expression analysis (edgeR), and tertiary analyses including Gene Ontology and pathway analysis, with support for paired-end and single-end data and multiple-group comparisons.