loci2path

This package is for version 3.21 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: 3.21

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 "4.5") 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")

loci2path HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BioCarta, Coverage, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Sequencing, Software

Version 1.28.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 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

Suggests BiocStyle, knitr, rmarkdown

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Package Archives

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

Source Package loci2path_1.28.0.tar.gz

Windows Binary (x86_64) loci2path_1.28.0.zip

macOS Binary (x86_64) loci2path_1.28.0.tgz

macOS Binary (arm64) loci2path_1.28.0.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/

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