GGtools

This package is for version 3.9 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

DOI: 10.18129/B9.bioc.GGtools

Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")

GGtools: software for eQTL identification PDF R Script

Reference Manual PDF

README Text

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, GeneticVariability, Genetics, SNP, Software

Version 5.20.0

In Bioconductor since BioC 1.9 (R-2.4) (17.5 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

System Requirements

URL

Suggests GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta

Linking To

Enhances MatrixEQTL, foreach, doParallel, gwascat

Depends On Me ceu1kg, eQTL

Imports Me ceuhm3, GeneGeneInteR

Suggests Me cgdv17, dsQTL, GGBase, gQTLBase, hmyriB36

Links To Me

Build Report Build Report

Package Archives

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

Source Package GGtools_5.20.0.tar.gz

Windows Binary GGtools_5.20.0.zip

Mac OS X 10.11 (El Capitan) GGtools_5.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/GGtools

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GGtools

Bioc Package Browser https://code.bioconductor.org/browse/GGtools/

Package Short Url https://bioconductor.org/packages/GGtools/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.9 Source Archive