trigger

DOI: 10.18129/B9.bioc.trigger    

Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Bioconductor version: Release (3.15)

This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.

Author: Lin S. Chen <lchen at health.bsd.uchicago.edu>, Dipen P. Sangurdekar <dps at genomics.princeton.edu> and John D. Storey <jstorey at princeton.edu>

Maintainer: John D. Storey <jstorey at princeton.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("trigger")

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("trigger")

 

PDF	R Script	Trigger Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneticVariability, Genetics, Microarray, SNP, Software
Version	1.42.0
In Bioconductor since	BioC 2.9 (R-2.14) (11 years)
License	GPL-3
Depends	R (>= 2.14.0), corpcor, qtl
Imports	qvalue, methods, graphics, sva
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Package Archives

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

Source Package	trigger_1.42.0.tar.gz
Windows Binary	trigger_1.42.0.zip
macOS Binary (x86_64)	trigger_1.42.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/trigger
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/trigger
Package Short Url	https://bioconductor.org/packages/trigger/
Package Downloads Report	Download Stats