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MODifieR: an ensemble R package for inference of disease modules from transcriptomics networks
University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden. (Translationell bioinformatik, Translational bioinformatics)ORCID iD: 0000-0001-7804-1177
University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden. (Translationell bioinformatik, Translational bioinformatics)ORCID iD: 0000-0002-6719-4861
Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden. (Translationell bioinformatik, Translational bioinformatics)ORCID iD: 0000-0002-9276-0546
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2020 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 36, no 12, p. 3918-3919Article in journal (Refereed) Published
Abstract [en]

MOTIVATION: Complex diseases are due to the dense interactions of many disease-associated factors that dysregulate genes that in turn form so-called disease modules, which have shown to be a powerful concept for understanding pathological mechanisms. There exist many disease module inference methods that rely on somewhat different assumptions, but there is still no gold standard or best performing method. Hence, there is a need for combining these methods to generate robust disease modules.

RESULTS: We developed MODule IdentiFIER (MODifieR), an ensemble R package of nine disease module inference methods from transcriptomics networks. MODifieR uses standardized input and output allowing the possibility to combine individual modules generated from these methods into more robust disease-specific modules, contributing to a better understanding of complex diseases.

AVAILABILITY: MODifieR is available under the GNU GPL license and can be freely downloaded from https://gitlab.com/Gustafsson-lab/MODifieR and as a Docker image from https://hub.docker.com/r/ddeweerd/modifier.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Place, publisher, year, edition, pages
Oxford University Press, 2020. Vol. 36, no 12, p. 3918-3919
National Category
Bioinformatics and Systems Biology
Research subject
Bioinformatics; INF501 Integration of -omics Data
Identifiers
URN: urn:nbn:se:his:diva-18387DOI: 10.1093/bioinformatics/btaa235ISI: 000550127500051PubMedID: 32271876Scopus ID: 2-s2.0-85087321319OAI: oai:DiVA.org:his-18387DiVA, id: diva2:1423798
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CC BY 4.0

"Applications Note". "Systems biology". 

Available from: 2020-04-15 Created: 2020-04-15 Last updated: 2022-04-13Bibliographically approved

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de Weerd, Hendrik A.Badam, Tejaswi V. S.Åkesson, JuliaLubovac-Pilav, Zelmina

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