eQTL

This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see eQTL.

Cloud-enabled cis-eQTL searches with Bioconductor GGtools 5.x

Bioconductor version: 3.8

This workflow focuses on searches for eQTL in cis, so that DNA variants local to the gene assayed for expression are tested for association.

Author: Vincent Carey [aut, cre]

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

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

Installation

To install this package, start R (version "3.5") and enter:


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

BiocManager::install("eQTL")

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("eQTL")

Cloud-enabled cis-eQTL searches with Bioconductor GGtools 5.x

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R Script

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GenomicVariantsWorkflow, Workflow
Version	1.4.0
License	Artistic-2.0
Depends	R (>= 3.3.0), GGdata, GGtools, GenomeInfoDb, S4Vectors, SNPlocs.Hsapiens.dbSNP144.GRCh37, bibtex, biglm, data.table, doParallel, foreach, knitcitations, lumi, lumiHumanAll.db, parallel, rmeta, scatterplot3d, snpStats, grid, yri1kgv
Imports
System Requirements
URL	https://www.bioconductor.org/help/workflows/eQTL/

Suggests	knitr, rmarkdown, BiocStyle
Linking To
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Package Archives

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

Source Package	eQTL_1.4.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/eQTL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/eQTL
Package Short Url	https://bioconductor.org/packages/eQTL/
Package Downloads Report	Download Stats