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qpgraph specifications

Information


Unique identifier OMICS_14610
Name qpgraph
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 2.14.0
Stability Stable
Requirements
AnnotationDbi, methods, parallel, grid, BiocGenerics, Biobase, IRanges, GenomicRanges, snow, S4Vectors, GenomeInfoDb, BiocStyle, BiocParallel, RUnit, GenomicFeatures, genefilter, mvtnorm, annotate, GOstats, Category, Rgraphviz, R(>=3.4), qtl, Matrix(>=1.0), graph(>=1.45.1), org.EcK12.eg.db, rlecuyer
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Robert Castelo

Publications for qpgraph

qpgraph citations

 (8)
library_books

Origins and genetic legacies of the Caribbean Taino

2018
Proc Natl Acad Sci U S A
PMCID: 5877975
PMID: 29463742
DOI: 10.1073/pnas.1716839115

[…] e analysis (SI Appendix, section 12). The direct ancestry test was also performed on the masked data (SI Appendix, section 16), and the admixture graphs ( and SI Appendix, Fig. S18) were fitted using qpGraph from the AdmixTools package () (SI Appendix, section 17). The ChromoPainter () analysis was run on the unmasked dataset (SI Appendix, Fig. S19). […]

library_books

The promise of disease gene discovery in South Asia

2017
Nat Genet
PMCID: 5675555
PMID: 28714977
DOI: 10.1038/ng.3917

[…] We used qpGraph to model each Indian group on the cline as a mixture of ANI and ASI ancestry, using the model (YRI, (Indian group, (Georgians, ANI)), [(ASI, Onge])) proposed by Moorjani et al. This approach p […]

library_books

Computational dynamic approaches for temporal omics data with applications to systems medicine

2017
BioData Min
PMCID: 5473988
PMID: 28638442
DOI: 10.1186/s13040-017-0140-x

[…] , protein, and metabolite data using more advanced biological-network-based approaches such as Gaussian graphical models, partial correlation and Bayesian networks for omics data integration (glasso, qpgraph). For instance, time-vaRying enriCHment integrOmics Subpathway aNalysis tOol (CHRONOS) is an R package built to extract regulatory sub-pathways along with their miRNA regulators at each time p […]

library_books

Ancient Genomics and the Peopling of the Southwest Pacific

2016
Nature
PMCID: 5515717
PMID: 27698418
DOI: 10.1038/nature19844

[…] overage ancient DNA data and is also often used for higher-coverage data to minimize reference genome biases that can be introduced when determining diploid genotypes,,,,,–. For the qpAdm, qpWave and qpGraph analyses we excluded transition SNPs to avoid biases from postmortem damage (see below).We performed PCA using smartpca, with the option inbreed: YES in order to sample a single genotype from […]

library_books

Genomic insights into the origin of farming in the ancient Near East

2016
Nature
PMCID: 5003663
PMID: 27459054
DOI: 10.1038/nature19310

[…] We carried out Admixture Graph modeling with the qpGraph software using Mbuti as an outgroup unless otherwise specified. […]

library_books

The propagation of perturbations in rewired bacterial gene networks

2015
Nat Commun
PMCID: 4703840
PMID: 26670742
DOI: 10.1038/ncomms10105

[…] by reverse engineering a transcriptional network from the gene expression microarray data. For this purpose, we used a Gaussian graphical modelling technique implemented in the R/Bioconductor package qpgraph. This method is based on higher-order conditioning to try to distinguish direct associations from indirect ones. The latter often occur owing to technical biases and strong genetic and molecul […]

Citations

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qpgraph institution(s)
Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain; Research Program on Biomedical Informatics, Institut Municipal d’Investigació Mèdica, Barcelona, Spain; Department of Statistical Science, Università di Bologna, Bologna, Italy
qpgraph funding source(s)
This work was supported by the Spanish Ministerio de Ciencia e Innovación (MICINN) (grant TIN2008-00556/TIN), by the ISCIII COMBIOMED Network (grant RD07/0067/0001), by a research fellowship of the Ramon y Cajal program from the Spanish MICINN (RYC-2006-000932) and by the Ministero dell’Università e della Ricerca (grant PRIN-2007AYHZWC, FISR MITICA).

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