loci2path
This package is for version 3.9 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: 3.9
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("loci2path")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | BioCarta, Coverage, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, Sequencing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4) |
| 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_1.4.0.tar.gz |
| Windows Binary | loci2path_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | loci2path_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/loci2path |
| Source Repository (Developer Access) | git clone [email protected]:packages/loci2path |
| Bioc Package Browser | https://code.bioconductor.org/browse/loci2path/ |
| Package Short Url | https://bioconductor.org/packages/loci2path/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |