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Bioinformatics. 2020 Jan 10. pii: btz858. doi: 10.1093/bioinformatics/btz858. [Epub ahead of print]

PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling.

Author information

1
Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne Switzerland.
2
Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne Switzerland.

Abstract

Protein phosphorylation - catalyzed by protein kinases - is the most common post-translational modification. It increases the functional diversity of the proteome and influences various aspects of normal physiology and can be altered in disease states. High throughput profiling of kinases is becoming an essential experimental approach to investigate their activity and this can be achieved using technologies such as PamChip® arrays provided by PamGene for kinase activity measurement. Here we present "pamgeneAnalyzeR", an R package developed as an alternative to the manual steps necessary to extract the data from PamChip® peptide microarrays images in a reproducible and robust manner. The extracted data can be directly used for downstream analysis.

AVAILABILITY AND IMPLEMENTATION:

PamgeneAnalyzeR is implemented in R and can be obtained from https://github.com/amelbek/pamgeneAnalyzeR.

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