gwascat

This is the development version of gwascat; for the stable release version, see gwascat.

representing and modeling data in the EMBL-EBI GWAS catalog

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DOI: 10.18129/B9.bioc.gwascat

Bioconductor version: Development (3.23)

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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 2.43.0

In Bioconductor since BioC 2.10 (R-2.15) (13.5 years)

License Artistic-2.0

Depends R (>= 4.1.0), methods

Imports S4Vectors(>= 0.9.25), IRanges, Seqinfo, GenomeInfoDb, GenomicRanges(>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub, data.table, tibble

System Requirements

URL

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 vtpnet, liftOver

Imports Me circRNAprofiler

Suggests Me GenomicScores, hmdbQuery, ldblock, parglms, TFutils, grasp2db

Links To Me

Build Report Build Report

Package Archives

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

Source Package gwascat_2.43.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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