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gwascat

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see gwascat.

representing and modeling data in the EMBL-EBI GWAS catalog


Bioconductor version: 3.16

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Genetics, Software
Version 2.30.0
In Bioconductor since BioC 2.10 (R-2.15) (12 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
System Requirements
URL
See More
Suggests DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle
Linking To
Enhances SNPlocs.Hsapiens.dbSNP144.GRCh37
Depends On Me liftOver, vtpnet
Imports Me circRNAprofiler
Suggests Me GenomicScores, grasp2db, hmdbQuery, ldblock, parglms, TFutils
Links To Me
Build Report Build Report

Package Archives

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

Source Package gwascat_2.30.0.tar.gz
Windows Binary gwascat_2.30.0.zip (64-bit only)
macOS Binary (x86_64) gwascat_2.30.0.tgz
macOS Binary (arm64) gwascat_2.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gwascat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gwascat
Bioc Package Browser https://code.bioconductor.org/browse/gwascat/
Package Short Url https://bioconductor.org/packages/gwascat/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive