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PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling.

Authors
  • Bekkar, Amel1
  • Nasrallah, Anita2
  • Guex, Nicolas1
  • Fajas, Lluis2
  • Xenarios, Ioannis2
  • Lopez-Mejia, Isabel C2
  • 1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland. , (Switzerland)
  • 2 Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland. , (Switzerland)
Type
Published Article
Journal
Bioinformatics (Oxford, England)
Publication Date
Dec 22, 2020
Volume
36
Issue
20
Pages
5117–5119
Identifiers
DOI: 10.1093/bioinformatics/btz858
PMID: 31922550
Source
Medline
Language
English
License
Unknown

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. PamgeneAnalyzeR is implemented in R and can be obtained from https://github.com/amelbek/pamgeneAnalyzeR. © The Author(s) 2020. Published by Oxford University Press.

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