gwascat

DOI: 10.18129/B9.bioc.gwascat    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see gwascat.

representing and modeling data in the EMBL-EBI GWAS catalog

Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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 2.16.1
In Bioconductor since BioC 2.10 (R-2.15) (7.5 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), GenomicFeatures, Biostrings, Rsamtools, rtracklayer, AnnotationDbi
LinkingTo
Suggests DO.db, DT, utils, knitr, RBGL, RUnit, snpStats, Gviz, VariantAnnotation, AnnotationHub, gQTLstats, graph, ggbio, ggplot2, DelayedArray
SystemRequirements
Enhances SNPlocs.Hsapiens.dbSNP144.GRCh37
URL
Depends On Me liftOver, vtpnet
Imports Me
Suggests Me GenomicScores, gQTLBase, gQTLstats, grasp2db, hmdbQuery, parglms, TFutils
Links To Me
Build Report  

Package Archives

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

Source Package gwascat_2.16.1.tar.gz
Windows Binary gwascat_2.16.1.zip
Mac OS X 10.11 (El Capitan) gwascat_2.16.1.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

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