loci2path

DOI: 10.18129/B9.bioc.loci2path    

This is the development version of loci2path; for the stable release version, see loci2path.

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

Bioconductor version: Development (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("loci2path", version = "devel")

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 1.1.1
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_1.1.1.tar.gz
Windows Binary loci2path_1.1.1.zip
Mac OS X 10.11 (El Capitan) loci2path_1.1.1.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 http://bioconductor.org/packages/loci2path/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: