title: CymeR: cytometry analysis using KNIME, docker and R.
abstract: Here we present open-source software for the analysis of high-dimensional cytometry data using state of the art algorithms. Importantly, use of the software requires no programming ability, and output files can either be interrogated directly in CymeR or they can be used downstream with any other cytometric data analysis platform. Also, because we use Docker to integrate the multitude of components that form the basis of CymeR, we have additionally developed a proof-of-concept of how future open-source bioinformatic programs with graphical user interfaces could be developed.
  
  
  
  CymeR is open-source software that ties several components into a single program that is perhaps best thought of as a self-contained data analysis operating system. Please see https://github.com/bmuchmore/CymeR/wiki for detailed installation instructions.
  
  
  
  brian.muchmore@genyo.es or marta.alarcon@genyo.es.
authors.affiliation: Centre for Genomics and Oncological Research (GENYO), Area of Genomic Medicine, Genetics of Complex Diseases, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Granada 18016, Spain.
authors.forename: B
authors.initials: B
authors.lastname: Muchmore
authors.affiliation: Centre for Genomics and Oncological Research (GENYO), Area of Genomic Medicine, Genetics of Complex Diseases, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Granada 18016, Spain.|IMM, Unit for Chronic Inflammatory Diseases, Karolinska Institutet, Stockholm 17177, Sweden.
authors.forename: M E
authors.initials: ME
authors.lastname: Alarcón-Riquelme
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D005434:Flow Cytometry / Q000379:methods*; D012984:Software