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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 languageEnglish (US)
Title of host publicationProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
EditorsIllhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages2157-2162
Number of pages6
ISBN (Electronic)9781509030491
DOIs
StatePublished - Dec 15 2017
Event2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States
Duration: Nov 13 2017Nov 16 2017

Publication series

NameProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume2017-January

Other

Other2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
CountryUnited States
CityKansas City
Period11/13/1711/16/17

Fingerprint

Immunology
Oncology
Formaldehyde
Gene expression
Paraffins
Data mining
Genes
Throughput
Multigene Family
Allergy and Immunology
Paraffin
Gene Expression
Datasets

Keywords

  • NanoString
  • clustering
  • differential gene expression
  • gene network
  • systems biology

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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.; Bhardwaj, Ratan D.; Gnimpieba, Etienne Z.

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 proceedingConference 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 C-R, 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). https://doi.org/10.1109/BIBM.2017.8217992
Hoffman, Mariah M. ; Minette, Carrie J. ; Messerli, Shanta M. ; Bhardwaj, Ratan D. ; Gnimpieba, Etienne Z. / 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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