loci2path

DOI: 10.18129/B9.bioc.loci2path    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see loci2path.

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Bioconductor version: 3.9

loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.

Author: Tianlei Xu

Maintainer: Tianlei Xu <tianlei.xu at emory.edu>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("loci2path")

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("loci2path")

 

HTML	R Script	loci2path
PDF		Reference Manual
Text		NEWS

Details

biocViews	BioCarta, Coverage, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Sequencing, Software
Version	1.4.0
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
License	Artistic-2.0
Depends	R (>= 3.4)
Imports	pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/StanleyXu/loci2path
BugReports	https://github.com/StanleyXu/loci2path/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	loci2path_1.4.0.tar.gz
Windows Binary	loci2path_1.4.0.zip
Mac OS X 10.11 (El Capitan)	loci2path_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/loci2path
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/loci2path
Package Short Url	https://bioconductor.org/packages/loci2path/
Package Downloads Report	Download Stats