PIPE-T

PIPE-T processes and analyzes microRNA (miR) expression profiles from reverse transcription quantitative PCR (RT-qPCR) data to produce reproducible results for downstream gene expression analyses.

Key Features:

• Galaxy workflow: Implemented as a Galaxy workflow developed using Galaxy workbench version 19.01.
• R package integration: Leverages functionalities from several R packages for data handling and analysis.
• Data processing: Provides parsing, filtering, normalization, imputation, and analysis specifically for RT-qPCR data.
• Input/output management: Accepts two input files and generates seven output files.
• Reproducibility: Enables reproducible and transparent execution of RT-qPCR analyses.

Scientific Applications:

• miR expression profiling: Processing and analysis of microRNA (miR) expression measured by RT-qPCR.
• RT-qPCR-based gene expression analysis: Generation of reproducible results for gene expression studies, with validation using datasets from the Gene Expression Omnibus (GEO).

Methodology:

Implemented as a Galaxy workflow that leverages R packages; computational steps explicitly include parsing, filtering, normalization, imputation, and analysis of RT-qPCR data, and the workflow was validated on two example datasets from GEO.