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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
NEWS Text

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
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Suggests BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package loci2path_1.23.0.tar.gz
Windows Binary loci2path_1.23.0.zip
macOS Binary (x86_64) loci2path_1.23.0.tgz
macOS Binary (arm64) loci2path_1.23.0.tgz
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