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Tools for Genome Wide Association Studies

Bioconductor version: Release (3.19)

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>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

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


biocViews GeneticVariability, Microarray, QualityControl, SNP, Software
Version 1.50.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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
See More
Suggests ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr
Linking To
Depends On Me mBPCR, GWASdata, snplinkage
Imports Me GENESIS, gwasurvivr
Suggests Me podkat
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package GWASTools_1.50.0.tar.gz
Windows Binary
macOS Binary (x86_64) GWASTools_1.50.0.tgz
macOS Binary (arm64) GWASTools_1.50.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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