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RCPA: An Open-Source R Package for Data Processing, Differential Analysis, Consensus Pathway Analysis, and

Hung Nguyen1,2, Ha Nguyen1,2, Zeynab Maghsoudi3

  • 1Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama.

Current Protocols
|May 7, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces RCPA, an R package simplifying pathway analysis for researchers. It integrates data processing, differential analysis, and multiple pathway analysis methods for robust biological insights across many species.

Keywords:
RNA sequencingdifferential analysisintegration and visualizationmicroarraypathway analysis

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Pathway analysis is crucial for understanding disease biology beyond gene expression.
  • Existing tools are complex, species-limited, and lack result integration capabilities.
  • Biomedical researchers face challenges with coding, command-line environments, and method selection.

Purpose of the Study:

  • To develop an accessible, open-source R package for comprehensive pathway analysis.
  • To address limitations in current pathway analysis tools regarding usability and species support.
  • To enable integrated analysis and comparison of results from diverse methods and datasets.

Main Methods:

  • Developed the R package Consensus Pathway Analysis (RCPA).
  • Integrated data processing from NCBI GEO for microarrays and RNA-Seq.
  • Implemented differential analysis, gene set enrichment, and topology-based pathway analysis.
  • Enabled combining methods and datasets for consensus results and visualization.

Main Results:

  • RCPA supports over 1000 species, multiple pathway databases, and various analysis techniques.
  • The package facilitates data integration, differential analysis, and pathway analysis.
  • It allows for combining and comparing results from different methods and experiments.
  • Provides visualization tools for exploring significantly impacted pathways.

Conclusions:

  • RCPA simplifies complex pathway analysis for a broader range of biomedical researchers.
  • The package enhances the ability to gain biological insights by integrating diverse analytical approaches.
  • RCPA supports cross-species analysis and robust hypothesis testing through consensus results.