Package: rqt 1.33.0

Ilya Zhbannikov

rqt: rqt: utilities for gene-level meta-analysis

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, <doi:10.1093/bioinformatics/btw429>.

Authors:Ilya Zhbannikov [aut, cre], Konstantin Arbeev [aut], Anatoliy Yashin [aut]

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NEWS

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

Peer review:

Bug tracker:https://github.com/izhbannikov/rqt/issues

On BioConductor:rqt-1.33.0(bioc 3.21)rqt-1.32.0(bioc 3.20)

genomewideassociationregressionsurvivalprincipalcomponentstatisticalmethodsequencing

4.30 score 2 stars 4 scripts 150 downloads 1 mentions 7 exports 145 dependencies

Last updated 2 months agofrom:4366457832. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 06 2024
R-4.5-winOKDec 06 2024
R-4.5-linuxOKDec 06 2024
R-4.4-winOKDec 06 2024
R-4.4-macOKDec 06 2024
R-4.3-winOKDec 06 2024
R-4.3-macOKDec 06 2024

Exports:covariatesgeneTestgeneTestMetagenotypephenotyperesultsrqt

Dependencies:abindaskpassbackportsbase64encBiobaseBiocBaseUtilsBiocGenericsbootbroombslibcachemcalibratecarcarDataclicodetoolscolorspaceCompQuadFormcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDEoptimRDerivdigestdoBydplyrevaluatefansifarverfastmapfontawesomeforeachFormulafsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelglmnetgluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelimmalme4magrittrMASSmathjaxrMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemetapmgcvmicrobenchmarkmimeminqamnormtmodelrmultcompMultiAssayExperimentMultiDataSetmulttestmunsellmutossmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotlyplotrixplspromisespurrrqqconfqqmanquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackrlangrmarkdownrobustbaseroplsRUnitS4ArraysS4VectorssandwichsassscalesshapesnSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsysTFisherTH.datatibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioczoo

Using RQT, an R package for gene-level meta-analysis

Ilya Y. Zhbannikov

Rendered fromrqt-vignette.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-08-01
Started: 2017-03-01