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

Need some help? Ask on the Bioconductor Support site!

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

Suggests	testthat, BiocStyle, knitr, covr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	multistateQTL_1.0.0.tar.gz
Windows Binary (x86_64)	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/
Package Downloads Report	Download Stats