Package: martini 1.33.0

Hector Climente-Gonzalez

martini: GWAS Incorporating Networks

martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.

Authors:Hector Climente-Gonzalez [aut, cre], Chloe-Agathe Azencott [aut]

martini_1.33.0.tar.gz
martini_1.33.0.zip(r-4.7-x86_64)martini_1.33.0.zip(r-4.7-arm64)martini_1.33.0.zip(r-4.6-x86_64)martini_1.33.0.zip(r-4.6-arm64)martini_1.33.0.zip(r-4.5-x86_64)
martini_1.33.0.tgz(r-4.6-x86_64)martini_1.33.0.tgz(r-4.6-arm64)martini_1.33.0.tgz(r-4.5-x86_64)martini_1.33.0.tgz(r-4.5-arm64)
martini_1.33.0.tar.gz(r-4.7-arm64)martini_1.33.0.tar.gz(r-4.7-x86_64)martini_1.33.0.tar.gz(r-4.6-arm64)martini_1.33.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
martini/json (API)

# Install 'martini' in R:
install.packages('martini', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hclimente/martini/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:martini-1.33.0(bioc 3.24)martini-1.32.0(bioc 3.23)

softwaregenomewideassociationsnpgeneticvariabilitygeneticsfeatureextractiongraphandnetworknetworkbioinformaticsgenomicsgwasnetwork-analysissnpssystems-biologycpp

6.05 score 4 stars 35 scripts 548 downloads 16 exports 20 dependencies

Last updated from:f8b9bd1355. Checks:1 WARNING, 13 ERROR, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING231
linux-devel-arm64ERROR558
linux-devel-x86_64ERROR565
source / vignettesOK350
linux-release-arm64ERROR542
linux-release-x86_64ERROR524
macos-release-arm64ERROR388
macos-release-x86_64ERROR735
macos-oldrel-arm64ERROR432
macos-oldrel-x86_64ERROR663
windows-devel-arm64ERROR506
windows-devel-x86_64ERROR524
windows-release-arm64ERROR520
windows-release-x86_64ERROR578
windows-oldrel-x86_64ERROR549
wasm-releaseFAIL311

Exports:get_GI_networkget_GM_networkget_GS_networkldweight_edgesplot_ideogramsconesscones_scones.cvscones.cv_search_conessigmodsigmod_sigmod.cvsigmod.cv_simulate_causal_snpssimulate_phenotype

Dependencies:BiocGenericscachemclicpp11fastmapgenericsglueigraphlatticelifecyclemagrittrMatrixmemoisepkgconfigRcppRcppEigenrlangsnpStatssurvivalvctrs

Running SConES
Experimental data | The network | References
Rendered fromscones_usage.Rmdusingknitr::rmarkdown

Last update: 2021-03-02
Started: 2017-07-13

Simulating SConES-based phenotypes
References
Rendered fromsimulate_phenotype.Rmdusingknitr::rmarkdown

Last update: 2021-03-02
Started: 2017-07-13