trigger
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Bioconductor version: Release (3.20)
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>
citation("trigger")
):
Installation
To install this package, start R (version "4.4") 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")
Trigger Tutorial | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | GeneExpression, GeneticVariability, Genetics, Microarray, SNP, Software |
Version | 1.52.0 |
In Bioconductor since | BioC 2.9 (R-2.14) (13 years) |
License | GPL-3 |
Depends | R (>= 2.14.0), corpcor, qtl |
Imports | qvalue, methods, graphics, sva |
System Requirements | |
URL |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | trigger_1.52.0.tar.gz |
Windows Binary (x86_64) | trigger_1.52.0.zip |
macOS Binary (x86_64) | trigger_1.52.0.tgz |
macOS Binary (arm64) | trigger_1.52.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/trigger |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/trigger |
Bioc Package Browser | https://code.bioconductor.org/browse/trigger/ |
Package Short Url | https://bioconductor.org/packages/trigger/ |
Package Downloads Report | Download Stats |