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dc.contributor.authorWatts, Stephen C
dc.contributor.authorRitchie, Scott C
dc.contributor.authorInouye, Michael
dc.contributor.authorHolt, Kathryn E
dc.date.accessioned2018-11-22T00:31:27Z
dc.date.available2018-11-22T00:31:27Z
dc.date.issued2019-03-15
dc.identifier.issn1367-4803
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/285621
dc.description.abstractSUMMARY: A common goal of microbiome studies is the elucidation of community composition and member interactions using counts of taxonomic units extracted from sequence data. Inference of interaction networks from sparse and compositional data requires specialized statistical approaches. A popular solution is SparCC, however its performance limits the calculation of interaction networks for very high-dimensional datasets. Here we introduce FastSpar, an efficient and parallelizable implementation of the SparCC algorithm which rapidly infers correlation networks and calculates P-values using an unbiased estimator. We further demonstrate that FastSpar reduces network inference wall time by 2-3 orders of magnitude compared to SparCC. AVAILABILITY AND IMPLEMENTATION: FastSpar source code, precompiled binaries and platform packages are freely available on GitHub: github.com/scwatts/FastSpar. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
dc.format.mediumPrint
dc.languageeng
dc.publisherOxford University Press (OUP)
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectAlgorithms
dc.subjectSoftware
dc.subjectMicrobiota
dc.titleFastSpar: rapid and scalable correlation estimation for compositional data.
dc.typeArticle
prism.endingPage1066
prism.issueIdentifier6
prism.publicationDate2019
prism.publicationNameBioinformatics
prism.startingPage1064
prism.volume35
dc.identifier.doi10.17863/CAM.32975
dcterms.dateAccepted2018-08-28
rioxxterms.versionofrecord10.1093/bioinformatics/bty734
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2019-03
dc.contributor.orcidRitchie, Scott [0000-0002-8454-9548]
dc.contributor.orcidInouye, Michael [0000-0001-9413-6520]
dc.identifier.eissn1367-4811
rioxxterms.typeJournal Article/Review
cam.issuedOnline2018-08-29


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International