GGtools

DOI: 10.18129/B9.bioc.GGtools    

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GGtools.

software and data for analyses in genetics of gene expression

Bioconductor version: 3.12

software and data for analyses in genetics of gene expression and/or DNA methylation

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

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

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("GGtools")

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("GGtools")

 

PDF	R Script	GGtools: software for eQTL identification
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	GeneExpression, GeneticVariability, Genetics, SNP, Software
Version	5.25.3
In Bioconductor since	BioC 1.9 (R-2.4) (14.5 years)
License	Artistic-2.0
Depends	R (>= 2.14), GGBase(>= 3.19.7), data.table, parallel, Homo.sapiens
Imports	methods, utils, stats, BiocGenerics(>= 0.25.1), snpStats, ff, Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin, rtracklayer, Gviz, stats4, S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges(>= 1.29.6), iterators, Biostrings, ROCR, biglm, ggplot2, reshape2
LinkingTo
Suggests	GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta
SystemRequirements
Enhances	MatrixEQTL, foreach, doParallel, gwascat
URL
Depends On Me	ceu1kg, eQTL
Imports Me	ceuhm3, GeneGeneInteR
Suggests Me	cgdv17, dsQTL, GGBase, hmyriB36
Links To Me
Build Report

Package Archives

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

Source Package	GGtools_5.25.3.tar.gz
Windows Binary	GGtools_5.25.3.zip
macOS 10.13 (High Sierra)	GGtools_5.25.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GGtools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GGtools
Package Short Url	https://bioconductor.org/packages/GGtools/
Package Downloads Report	Download Stats