- Home
- Bioconductor 3.0
- Software Packages
- GWASTools
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GWASTools")
In most cases, you don't need to download the package archive at all.
GWASTools
Tools for Genome Wide Association Studies
Bioconductor version: 3.0
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, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar, Adrienne Stilp
Maintainer: Stephanie M. Gogarten <sdmorris at u.washington.edu>, Adrienne Stilp <amstilp at u.washington.edu>
Citation (from within R,
enter citation("GWASTools")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GWASTools")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GWASTools")
| R Script | Data formats in GWASTools | |
| R Script | GWAS Data Cleaning | |
| R Script | Preparing Affymetrix Data | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneticVariability, Microarray, QualityControl, SNP, Software |
| Version | 1.12.2 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | Artistic-2.0 |
| Depends | Biobase, ncdf, gdsfmt |
| Imports | methods, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, quantsmooth |
| LinkingTo | |
| Suggests | GWASdata, BiocGenerics, RUnit, SNPRelate, snpStats, VariantAnnotation |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | GWASdata |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GWASTools_1.12.2.tar.gz |
| Windows Binary | GWASTools_1.12.2.zip |
| Mac OS X 10.6 (Snow Leopard) | GWASTools_1.12.2.tgz |
| Mac OS X 10.9 (Mavericks) | GWASTools_1.12.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
