gwascat

DOI: 10.18129/B9.bioc.gwascat    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see gwascat.

representing and modeling data in the EMBL-EBI GWAS catalog

Bioconductor version: 3.15

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 "4.2") and enter:

if (!require("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")

 

HTML	R Script	gwascat -- GRanges for GWAS hits in EBI catalog
HTML	R Script	gwascat: structuring and querying the NHGRI GWAS catalog
PDF		Reference Manual
Text		NEWS

Details

biocViews	Genetics, Software
Version	2.28.1
In Bioconductor since	BioC 2.10 (R-2.15) (10.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), methods
Imports	S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges(>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub
LinkingTo
Suggests	DO.db, DT, knitr, RBGL, testthat, rmarkdown, Gviz, Rsamtools, IRanges, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle
SystemRequirements
Enhances	SNPlocs.Hsapiens.dbSNP144.GRCh37
URL
Depends On Me	liftOver, vtpnet
Imports Me	circRNAprofiler
Suggests Me	GenomicScores, grasp2db, hmdbQuery, ldblock, parglms, TFutils
Links To Me
Build Report

Package Archives

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

Source Package	gwascat_2.28.1.tar.gz
Windows Binary	gwascat_2.28.1.zip (64-bit only)
macOS Binary (x86_64)	gwascat_2.28.1.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	https://bioconductor.org/packages/gwascat/
Package Downloads Report	Download Stats