GWASTools
This is the development version of GWASTools; for the stable release version, see GWASTools.
Tools for Genome Wide Association Studies
Bioconductor version: Development (3.24)
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("GWASTools")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| Data formats in GWASTools | R Script | |
| GWAS Data Cleaning | R Script | |
| Preparing Affymetrix Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 |
See More
| Suggests | ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | mBPCR, GWASdata, snplinkage |
| Imports Me | GENESIS, gwasurvivr |
| Suggests Me | podkat |
| Links To Me | |
| Build Report | Build Report |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/GWASTools/ |
| Package Short Url | https://bioconductor.org/packages/GWASTools/ |
| Package Downloads Report | Download Stats |