GWASTools

This is the development version of GWASTools; for the stable release version, see GWASTools.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

Tools for Genome Wide Association Studies

Bioconductor version: Development (3.24)

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

Author: Stephanie M. Gogarten [aut], Cathy Laurie [aut], Tushar Bhangale [aut], Matthew P. Conomos [aut], Cecelia Laurie [aut], Michael Lawrence [aut], Caitlin McHugh [aut], Ian Painter [aut], Xiuwen Zheng [aut], Jess Shen [aut], Rohit Swarnkar [aut], Adrienne Stilp [aut], Sarah Nelson [aut], David Levine [aut], Sonali Kumari [ctb] (Converted vignettes from Sweave to RMarkdown / HTML.), Stephanie M. Gogarten [cre]

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

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

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. GWASTools: Tools for Genome Wide Association Studies. doi:10.18129/B9.bioc.GWASTools, R package version 1.59.0, https://bioconductor.org/packages/GWASTools.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneticVariability, Microarray, QualityControl, SNP, Software
Version	1.59.0
In Bioconductor since	BioC 2.9 (R-2.14) (15 years)
License	Artistic-2.0
Depends	Biobase
Imports	graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table
System Requirements
URL	https://github.com/smgogarten/GWASTools

Suggests	ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr
Linking To
Enhances
Depends On Me	GWASdata, mBPCR, snplinkage
Imports Me	GENESIS, gwasurvivr
Suggests Me	podkat
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	GWASTools_1.59.0.tar.gz
Windows Binary (x86_64)	GWASTools_1.59.0.zip
macOS Binary (big-sur-x86_64)	GWASTools_1.59.0.tgz
macOS Binary (sonoma-arm64)	GWASTools_1.59.0.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