Package: multistateQTL 1.3.0

Amelia Dunstone

multistateQTL: Toolkit for the analysis of multi-state QTL data

A collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package 'multistateQTL' contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a 'QTLExperiment' object, which is based on the 'SummarisedExperiment' framework.

Authors:Christina Del Azodi [aut], Davis McCarthy [ctb], Amelia Dunstone [cre, ctb]

multistateQTL_1.3.0.tar.gz
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multistateQTL_1.3.0.tgz(r-4.4-any)multistateQTL_1.3.0.tgz(r-4.3-any)
multistateQTL_1.3.0.tar.gz(r-4.5-noble)multistateQTL_1.3.0.tar.gz(r-4.4-noble)
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multistateQTL.pdf |multistateQTL.html✨
multistateQTL/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/dunstone-a/multistateqtl/issues

On BioConductor:multistateQTL-1.3.0(bioc 3.21)multistateQTL-1.2.0(bioc 3.20)

functionalgenomicsgeneexpressionsequencingvisualizationsnpsoftware

4.65 score 9 scripts 128 downloads 18 exports 107 dependencies

Last updated 2 months agofrom:d831d40dd9. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macERRORNov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macERRORNov 29 2024

Exports:callSignificancecallSignificance<-getCompletegetSignificantgetTopHitsplotCompareStatesplotPairwiseSharingplotQTLClustersplotSimulationParamsplotUpSetqtleEstimateqtleParamsqtleSimulatereplaceNAsrunPairwiseSharingrunSignificantFeaturesrunTestMetricssimPerformance

Dependencies:abindashraskpassassertthatbackportsBiobaseBiocGenericsbitbit64checkmatecirclizecliclueclustercodetoolscollapsecolorspaceComplexHeatmapcpp11crayoncurldata.tableDelayedArraydigestdoParalleldplyretrunctfansifarverfitdistrplusforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegridExtragtablehmshttrinvgammaIRangesirlbaisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrmashrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemixsqpmunsellmvtnormnlmeopensslpillarpkgconfigplyrpngprettyunitsprogresspurrrQTLExperimentR6RColorBrewerRcppRcppArmadilloRcppGSLrjsonrlangrmetaS4ArraysS4VectorsscalesshapesoftImputeSparseArraySQUAREMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttruncnormtzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrXVectorzlibbioc

multistateQTL: Orchestrating multi-state QTL analysis in R

Christina B Azodi, Davis McCarthy, Amelia Dunstone

Rendered frommultiStateQTL.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-04-21
Started: 2022-11-09