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


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

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
See More
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