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dc.contributor.authorWan, Ying-Wooi
Allen, Genevera I
Baker, Yulia
Yang, Eunho
Ravikumar, Pradeep
Anderson, Matthew
Liu, Zhandong
dc.date.accessioned 2016-08-26T16:02:12Z
dc.date.available 2016-08-26T16:02:12Z
dc.date.issued 2016
dc.identifier.citation Wan, Ying-Wooi, Allen, Genevera I, Baker, Yulia, et al.. "XMRF: an R package to fit Markov Networks to high-throughput genetics data." BMC Systems Biology, 10 (Suppl 3), (2016) http://dx.doi.org/10.1186/s12918-016-0313-0.
dc.identifier.urihttps://hdl.handle.net/1911/91358
dc.description.abstractAbstract Background Technological advances in medicine have led to a rapid proliferation of high-throughput “omics” data. Tools to mine this data and discover disrupted disease networks are needed as they hold the key to understanding complicated interactions between genes, mutations and aberrations, and epi-genetic markers. Results We developed an R software package, XMRF, that can be used to fit Markov Networks to various types of high-throughput genomics data. Encoding the models and estimation techniques of the recently proposed exponential family Markov Random Fields (Yang et al., 2012), our software can be used to learn genetic networks from RNA-sequencing data (counts via Poisson graphical models), mutation and copy number variation data (categorical via Ising models), and methylation data (continuous via Gaussian graphical models). Conclusions XMRF is the only tool that allows network structure learning using the native distribution of the data instead of the standard Gaussian. Moreover, the parallelization feature of the implemented algorithms computes the large-scale biological networks efficiently. XMRF is available from CRAN and Github ( https://github.com/zhandong/XMRF ).
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.title XMRF: an R package to fit Markov Networks to high-throughput genetics data
dc.type Journal article
dc.citation.journalTitle BMC Systems Biology
dc.citation.volumeNumber 10 (Suppl 3)
dc.contributor.publisher BioMed Central
dc.date.updated 2016-08-26T16:02:12Z
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1186/s12918-016-0313-0
dc.language.rfc3066 en
dc.type.publication publisher version
dcterms.bibliographicCitation BMC Systems Biology. 2016 Aug 26;10(Suppl 3):69
dc.rights.holder The Author(s)
local.sword.agent BioMed Central
dc.citation.articleNumber 69


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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.