Registration and Call for Abstracts Open for Bioc2024

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 (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
loci2path HTML R Script
Reference Manual PDF

Details

biocViews BioCarta, Coverage, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Sequencing, Software
Version 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors
System Requirements
URL https://github.com/StanleyXu/loci2path
Bug Reports https://github.com/StanleyXu/loci2path/issues
See More
Suggests BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package loci2path_1.23.0.tar.gz
Windows Binary
macOS Binary (x86_64) loci2path_1.23.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/loci2path
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/loci2path
Bioc Package Browser https://code.bioconductor.org/browse/loci2path/
Package Short Url https://bioconductor.org/packages/loci2path/
Package Downloads Report Download Stats