loci2path

DOI: 10.18129/B9.bioc.loci2path    

This package is for version 3.14 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: 3.14

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>

Citation (from within R, enter citation("loci2path")):

Installation

To install this package, start R (version "4.1") and enter:

if (!require("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")

 

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Details

biocViews BioCarta, Coverage, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.7 (R-3.5) (4 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_1.14.0.tar.gz
Windows Binary loci2path_1.14.0.zip
macOS 10.13 (High Sierra) loci2path_1.14.0.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/
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