trigger
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Bioconductor version: Release (3.19)
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 | 1.50.0 |
| 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 |
See More
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| Enhances | |
| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | trigger_1.50.0.tar.gz |
| Windows Binary (x86_64) | trigger_1.50.0.zip |
| macOS Binary (x86_64) | trigger_1.50.0.tgz |
| macOS Binary (arm64) | trigger_1.50.0.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 |