PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling
Amel Bekkar1, Anita Nasrallah2, Nicolas Guex1
1Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland.
Bioinformatics (Oxford, England)
|January 11, 2020
Summary
This study introduces pamgeneAnalyzeR, an R package for reproducible data extraction from PamChip® kinase activity arrays. It simplifies kinase profiling, aiding research into phosphorylation
Area of Science:
- Biochemistry
- Molecular Biology
- Bioinformatics
Background:
- Protein phosphorylation is a key post-translational modification regulating cellular functions.
- Altered kinase activity is implicated in various disease states.
- High-throughput kinase activity profiling is crucial for biological research and disease investigation.
Purpose of the Study:
- To present pamgeneAnalyzeR, an R package designed to automate data extraction from PamChip® peptide microarrays.
- To provide a reproducible and robust alternative to manual data extraction methods.
- To facilitate downstream analysis of kinase activity data.
Main Methods:
- Development of an R package named pamgeneAnalyzeR.
- Utilizing R programming language for implementation.
- Focusing on data extraction from PamChip® microarray images.
Main Results:
- pamgeneAnalyzeR enables reproducible and robust extraction of data from PamChip® peptide microarrays.
- The package streamlines the process, reducing manual effort.
- Extracted data is readily available for subsequent analyses.
Conclusions:
- pamgeneAnalyzeR offers an efficient solution for processing PamChip® data.
- The R package enhances the accessibility and usability of kinase activity profiling data.
- This tool supports research in phosphorylation and kinase activity studies.
