Auto-qPCR

Auto-qPCR automates processing of quantitative real-time PCR (qPCR) result spreadsheets to perform calculations and analyses for DNA quantification and gene expression (absolute and relative) studies.

Key Features:

• Automated qPCR calculations: Performs calculations typically done manually for qPCR analysis.
• Input handling: Processes result spreadsheets generated by thermal cycler machines.
• Implementation: Implemented in Python and provided as a command-line utility.
• DNA Quantification mode: Identifies genomic deletion or duplication events by quantifying DNA levels.
• Gene Expression Assessment (Absolute Model) mode: Evaluates gene expression levels using an absolute quantification model.
• Relative Quantification with Reference Sample mode: Compares gene expression levels relative to a reference sample for differential expression analysis.
• Relative Quantification without Reference Sample mode: Performs relative quantification workflows when no reference sample is available.
• Statistical analyses: Executes statistical analyses tailored to each processing mode.
• Data treatment and reporting: Provides data treatment and reporting options for processed qPCR results.
• Workflow automation: Automates systematic qPCR data-processing workflows to reduce manual steps and potential errors.

Scientific Applications:

• Genomic copy-number analysis: Detection of genomic deletion or duplication events via DNA quantification.
• Absolute gene expression quantification: Quantification of transcript levels using an absolute model.
• Relative differential expression with reference: Comparative gene expression analysis using a reference sample for differential expression studies.
• Relative quantification without reference: Comparative gene expression analysis when no reference sample is available.
• Pipeline integration: Integration into bioinformatics and molecular biology pipelines for research and clinical qPCR-based studies, including clinical diagnostics.

Methodology:

Processes thermal cycler result spreadsheets, applies automated qPCR calculations for absolute and relative quantification modes, and executes statistical analyses tailored to each mode.