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meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.

Publication ,  Journal Article
Gelfman, S; Wang, Q; Lu, Y-F; Hall, D; Bostick, CD; Dhindsa, R; Halvorsen, M; McSweeney, KM; Cotterill, E; Edinburgh, T; Beaumont, MA ...
Published in: PLoS Comput Biol
October 2018

Here we present an open-source R package 'meaRtools' that provides a platform for analyzing neuronal networks recorded on Microelectrode Arrays (MEAs). Cultured neuronal networks monitored with MEAs are now being widely used to characterize in vitro models of neurological disorders and to evaluate pharmaceutical compounds. meaRtools provides core algorithms for MEA spike train analysis, feature extraction, statistical analysis and plotting of multiple MEA recordings with multiple genotypes and treatments. meaRtools functionality covers novel solutions for spike train analysis, including algorithms to assess electrode cross-correlation using the spike train tiling coefficient (STTC), mutual information, synchronized bursts and entropy within cultured wells. Also integrated is a solution to account for bursts variability originating from mixed-cell neuronal cultures. The package provides a statistical platform built specifically for MEA data that can combine multiple MEA recordings and compare extracted features between different genetic models or treatments. We demonstrate the utilization of meaRtools to successfully identify epilepsy-like phenotypes in neuronal networks from Celf4 knockout mice. The package is freely available under the GPL license (GPL> = 3) and is updated frequently on the CRAN web-server repository. The package, along with full documentation can be downloaded from: https://cran.r-project.org/web/packages/meaRtools/.

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Published In

PLoS Comput Biol

DOI

EISSN

1553-7358

Publication Date

October 2018

Volume

14

Issue

10

Start / End Page

e1006506

Location

United States

Related Subject Headings

  • Software
  • Neurons
  • Microelectrodes
  • Mice, Knockout
  • Mice
  • Electrophysiology
  • Computational Biology
  • Cells, Cultured
  • Bioinformatics
  • Animals
 

Citation

APA
Chicago
ICMJE
MLA
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Gelfman, S., Wang, Q., Lu, Y.-F., Hall, D., Bostick, C. D., Dhindsa, R., … Eglen, S. J. (2018). meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays. PLoS Comput Biol, 14(10), e1006506. https://doi.org/10.1371/journal.pcbi.1006506
Gelfman, Sahar, Quanli Wang, Yi-Fan Lu, Diana Hall, Christopher D. Bostick, Ryan Dhindsa, Matt Halvorsen, et al. “meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.PLoS Comput Biol 14, no. 10 (October 2018): e1006506. https://doi.org/10.1371/journal.pcbi.1006506.
Gelfman S, Wang Q, Lu Y-F, Hall D, Bostick CD, Dhindsa R, et al. meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays. PLoS Comput Biol. 2018 Oct;14(10):e1006506.
Gelfman, Sahar, et al. “meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.PLoS Comput Biol, vol. 14, no. 10, Oct. 2018, p. e1006506. Pubmed, doi:10.1371/journal.pcbi.1006506.
Gelfman S, Wang Q, Lu Y-F, Hall D, Bostick CD, Dhindsa R, Halvorsen M, McSweeney KM, Cotterill E, Edinburgh T, Beaumont MA, Frankel WN, Petrovski S, Allen AS, Boland MJ, Goldstein DB, Eglen SJ. meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays. PLoS Comput Biol. 2018 Oct;14(10):e1006506.

Published In

PLoS Comput Biol

DOI

EISSN

1553-7358

Publication Date

October 2018

Volume

14

Issue

10

Start / End Page

e1006506

Location

United States

Related Subject Headings

  • Software
  • Neurons
  • Microelectrodes
  • Mice, Knockout
  • Mice
  • Electrophysiology
  • Computational Biology
  • Cells, Cultured
  • Bioinformatics
  • Animals