NanoStringBioNet: Integrated R framework for bioscience knowledge discovery from NanoString nCounter data

Mariah M. Hoffman; Carrie J. Minette; Shanta M. Messerli; Ratan D. Bhardwaj; Etienne Z. Gnimpieba

doi:10.1109/BIBM.2017.8217992

NanoStringBioNet: Integrated R framework for bioscience knowledge discovery from NanoString nCounter data

Mariah M. Hoffman, Carrie J. Minette, Shanta M. Messerli, Ratan D. Bhardwaj, Etienne Z. Gnimpieba

Great Plains IDeA-CTR

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

Abstract

The NanoString nCounter Analysis System is a medium-throughput gene expression quantification technique that is becoming increasingly popular in the fields of immunology and oncology due to its ease of use and sensitivity, particularly in the analysis of formalin-fixed paraffin embedded samples. Despite the growing interest in NanoString, systematic analysis frameworks for the reproducible analysis of nCounter data remain limited. NanoStringBioNet is a pair of R packages that form a semi-automatic, open source framework for integrative and systematic knowledge discovery from nCounter datasets. Using the NSData module, NanoStringBioNet preprocesses a raw NanoString dataset and stores it in Biobase format for sharability. Subsequently, the NSFunc module performs downstream analyses such as enrichment and network inference of stable differentially expressed gene clusters by leveraging existing data analysis tools and custom script.

Original language	English (US)
Title of host publication	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Editors	Illhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	2157-2162
Number of pages	6
ISBN (Electronic)	9781509030491
DOIs	https://doi.org/10.1109/BIBM.2017.8217992
State	Published - Dec 15 2017
Event	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States Duration: Nov 13 2017 → Nov 16 2017

Publication series

Name	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume	2017-January

Other

Other	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Country/Territory	United States
City	Kansas City
Period	11/13/17 → 11/16/17

Keywords

NanoString
clustering
differential gene expression
gene network
systems biology

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics

Access to Document

10.1109/BIBM.2017.8217992

Cite this

Hoffman, M. M., Minette, C. J., Messerli, S. M., Bhardwaj, R. D., & Gnimpieba, E. Z. (2017). NanoStringBioNet: Integrated R framework for bioscience knowledge discovery from NanoString nCounter data. In I. Yoo, J. H. Zheng, Y. Gong, X. T. Hu, C.-R. Shyu, Y. Bromberg, J. Gao, & D. Korkin (Eds.), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (pp. 2157-2162). (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217992

NanoStringBioNet: Integrated R framework for bioscience knowledge discovery from NanoString nCounter data. / Hoffman, Mariah M.; Minette, Carrie J.; Messerli, Shanta M. et al.
Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. ed. / Illhoi Yoo; Jane Huiru Zheng; Yang Gong; Xiaohua Tony Hu; Chi-Ren Shyu; Yana Bromberg; Jean Gao; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. p. 2157-2162 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Hoffman, MM, Minette, CJ, Messerli, SM, Bhardwaj, RD & Gnimpieba, EZ 2017, NanoStringBioNet: Integrated R framework for bioscience knowledge discovery from NanoString nCounter data. in I Yoo, JH Zheng, Y Gong, XT Hu, C-R Shyu, Y Bromberg, J Gao & D Korkin (eds), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 2157-2162, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 11/13/17. https://doi.org/10.1109/BIBM.2017.8217992

Hoffman MM, Minette CJ, Messerli SM, Bhardwaj RD, Gnimpieba EZ. NanoStringBioNet: Integrated R framework for bioscience knowledge discovery from NanoString nCounter data. In Yoo I, Zheng JH, Gong Y, Hu XT, Shyu CR, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc. 2017. p. 2157-2162. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017). doi: 10.1109/BIBM.2017.8217992

Hoffman, Mariah M. ; Minette, Carrie J. ; Messerli, Shanta M. et al. / NanoStringBioNet : Integrated R framework for bioscience knowledge discovery from NanoString nCounter data. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. editor / Illhoi Yoo ; Jane Huiru Zheng ; Yang Gong ; Xiaohua Tony Hu ; Chi-Ren Shyu ; Yana Bromberg ; Jean Gao ; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 2157-2162 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017).

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NanoStringBioNet: Integrated R framework for bioscience knowledge discovery from NanoString nCounter data

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Keywords

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