XMRF: an R package to fit Markov Networks to high-throughput genetics data

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dc.citation.articleNumber69en_US
dc.citation.journalTitleBMC Systems Biologyen_US
dc.citation.volumeNumber10 (Suppl 3)en_US
dc.contributor.authorWan, Ying-Wooien_US
dc.contributor.authorAllen, Genevera Ien_US
dc.contributor.authorBaker, Yuliaen_US
dc.contributor.authorYang, Eunhoen_US
dc.contributor.authorRavikumar, Pradeepen_US
dc.contributor.authorAnderson, Matthewen_US
dc.contributor.authorLiu, Zhandongen_US
dc.date.accessioned2016-08-26T16:02:12Zen_US
dc.date.available2016-08-26T16:02:12Zen_US
dc.date.issued2016en_US
dc.date.updated2016-08-26T16:02:12Zen_US
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 ).en_US
dc.identifier.citationWan, Ying-Wooi, Allen, Genevera I, Baker, Yulia, et al.. "XMRF: an R package to fit Markov Networks to high-throughput genetics data." <i>BMC Systems Biology,</i> 10 (Suppl 3), (2016) BioMed Central: http://dx.doi.org/10.1186/s12918-016-0313-0.en_US
dc.identifier.doihttp://dx.doi.org/10.1186/s12918-016-0313-0en_US
dc.identifier.urihttps://hdl.handle.net/1911/91358en_US
dc.language.isoengen_US
dc.publisherBioMed Centralen_US
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.en_US
dc.rights.holderThe Author(s)en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleXMRF: an R package to fit Markov Networks to high-throughput genetics dataen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
local.sword.agentBioMed Centralen_US
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