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GWASTools

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

Tools for Genome Wide Association Studies

Bioconductor version: Development (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
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")
Data formats in GWASTools PDF R Script
GWAS Data Cleaning PDF R Script
Preparing Affymetrix Data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneticVariability, Microarray, QualityControl, SNP, Software
Version 1.47.1
In Bioconductor since BioC 2.9 (R-2.14) (12 years)
License Artistic-2.0
Depends Biobase
Imports graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table
Linking To
Suggests ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr
System Requirements
Enhances
URL https://github.com/smgogarten/GWASTools
See More
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_1.47.1.tar.gz
Windows Binary GWASTools_1.47.1.zip
macOS Binary (x86_64) GWASTools_1.47.1.tgz
macOS Binary (arm64) GWASTools_1.47.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GWASTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GWASTools
Bioc Package Browser https://code.bioconductor.org/browse/GWASTools/
Package Short Url https://bioconductor.org/packages/GWASTools/
Package Downloads Report Download Stats