multistateQTL

Toolkit for the analysis of multi-state QTL data


Bioconductor version: Release (3.19)

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.

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

Maintainer: Amelia Dunstone <amelia.dunstone at svi.edu.au>

Citation (from within R, enter citation("multistateQTL")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("multistateQTL")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("multistateQTL")
multistateQTL: Orchestrating multi-state QTL analysis in R HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews FunctionalGenomics, GeneExpression, SNP, Sequencing, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3
Depends QTLExperiment, SummarizedExperiment, ComplexHeatmap, data.table, collapse
Imports methods, S4Vectors, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices
System Requirements
URL https://github.com/dunstone-a/multistateQTL
Bug Reports https://github.com/dunstone-a/multistateQTL/issues
See More
Suggests testthat, BiocStyle, knitr, covr, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package multistateQTL_1.0.0.tar.gz
Windows Binary multistateQTL_1.0.0.zip
macOS Binary (x86_64) multistateQTL_1.0.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/multistateQTL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/multistateQTL
Bioc Package Browser https://code.bioconductor.org/browse/multistateQTL/
Package Short Url https://bioconductor.org/packages/multistateQTL/
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