GWASTools

DOI: 10.18129/B9.bioc.GWASTools    

Tools for Genome Wide Association Studies

Bioconductor version: Release (3.13)

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Author: Stephanie M. Gogarten, Cathy Laurie, Tushar Bhangale, Matthew P. Conomos, Cecelia Laurie, Michael Lawrence, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar, Adrienne Stilp, Sarah Nelson, David Levine

Maintainer: Stephanie M. Gogarten <sdmorris at uw.edu>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("GWASTools")

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("GWASTools")

 

PDF	R Script	Data formats in GWASTools
PDF	R Script	GWAS Data Cleaning
PDF	R Script	Preparing Affymetrix Data
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneticVariability, Microarray, QualityControl, SNP, Software
Version	1.38.0
In Bioconductor since	BioC 2.9 (R-2.14) (10 years)
License	Artistic-2.0
Depends	Biobase
Imports	graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table
LinkingTo
Suggests	ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel
SystemRequirements
Enhances
URL	https://github.com/smgogarten/GWASTools
Depends On Me	GWASdata, mBPCR
Imports Me	GENESIS, gwasurvivr
Suggests Me	podkat
Links To Me
Build Report

Package Archives

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

Source Package	GWASTools_1.38.0.tar.gz
Windows Binary	GWASTools_1.38.0.zip
macOS 10.13 (High Sierra)	GWASTools_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GWASTools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GWASTools
Package Short Url	https://bioconductor.org/packages/GWASTools/
Package Downloads Report	Download Stats