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multistateQTL

Toolkit for the analysis of multi-state QTL data

Bioconductor version: 3.23 · Package version: 2.4.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("multistateQTL")

Details

MaintainerAmelia Dunstone <amelia.dunstone@svi.edu.au>
AuthorChristina Del Azodi [aut], Davis McCarthy [ctb], Amelia Dunstone [cre, aut] (ORCID: <https://orcid.org/0009-0009-6426-1529>)
LicenseGPL-3
URLhttps://github.com/dunstone-a/multistateQTL
Bug Reportshttps://github.com/dunstone-a/multistateQTL/issues
Downloads rank175
Source branchRELEASE_3_23
biocViewsFunctionalGenomics, GeneExpression, SNP, Sequencing, Software, Visualization

Documentation

Download

Dependencies

Depends: QTLExperiment, SummarizedExperiment, ComplexHeatmap, collapse

Imports: methods, S4Vectors, data.table, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices

Suggests: testthat, BiocStyle, knitr, covr, rmarkdown