gwascat

DOI: 10.18129/B9.bioc.gwascat    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see gwascat.

representing and modeling data in the EMBL-EBI GWAS catalog

Bioconductor version: 3.8

Represent and model data in the EMBL-EBI GWAS catalog.

Author: VJ Carey <stvjc at channing.harvard.edu>

Maintainer: VJ Carey <stvjc at channing.harvard.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("gwascat")

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("gwascat")

 

PDF	R Script	gwascat -- exploring NHGRI GWAS catalog
HTML	R Script	gwascat -- GRanges for GWAS hits in EBI catalog
PDF		Reference Manual
Text		NEWS

Details

biocViews	Genetics, Software
Version	2.14.0
In Bioconductor since	BioC 2.10 (R-2.15) (7 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), Homo.sapiens
Imports	methods, BiocGenerics, S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges(>= 1.29.6), snpStats, Biostrings, Rsamtools, rtracklayer, gQTLstats, Gviz, VariantAnnotation, AnnotationHub, AnnotationDbi, GenomicFeatures, graph, ggbio, ggplot2, SummarizedExperiment
LinkingTo
Suggests	DO.db, DT, utils, knitr, RBGL, RUnit
SystemRequirements
Enhances	SNPlocs.Hsapiens.dbSNP144.GRCh37
URL
Depends On Me	liftOver, vtpnet
Imports Me
Suggests Me	GenomicScores, gQTLBase, gQTLstats, grasp2db, hmdbQuery, TFutils
Links To Me
Build Report

Package Archives

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

Source Package	gwascat_2.14.0.tar.gz
Windows Binary	gwascat_2.14.0.zip
Mac OS X 10.11 (El Capitan)	gwascat_2.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gwascat
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gwascat
Package Short Url	http://bioconductor.org/packages/gwascat/
Package Downloads Report	Download Stats