qRAT - qPCR relative expression analysis tool

qRAT performs automated processing of raw Quantification Cycle (Cq) files from various qPCR instruments to compute relative quantities and fold changes for RT-qPCR-based gene expression analysis.

Key Features:

• Implementation: Implemented in R.
• Raw Cq parsing: Parses raw Quantification Cycle (Cq) data files from various qPCR instruments.
• Data filtering: Applies filtering and quality-control steps to Cq data.
• Normalization: Performs normalization of RT-qPCR data for relative quantification.
• Relative quantification and fold-change calculation: Computes relative quantities and fold changes for differentially expressed genes.
• Inter-plate variation correction: Corrects inter-plate variation across multi-plate experiments.
• Statistical methods: Applies well-established statistical methods for analysis.
• Visualization: Generates graphical visualizations using state-of-the-art graphical techniques.

Scientific Applications:

• Microbiology research: Detects transcriptional changes by comparing gene expression levels across samples using RT-qPCR.
• Relative quantification studies: Supports computation of relative quantities and fold changes in gene expression experiments.

Methodology:

Parsing, filtering, normalization, visualization of RT-qPCR Cq data; calculation of relative quantities and fold changes; correction of inter-plate variation; application of well-established statistical methods and graphical techniques; validated using two laboratory-generated example datasets.