LOLA

DOI: 10.18129/B9.bioc.LOLA    

Locus overlap analysis for enrichment of genomic ranges

Bioconductor version: Release (3.15)

Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.

Author: Nathan Sheffield <http://www.databio.org> [aut, cre], Christoph Bock [ctb]

Maintainer: Nathan Sheffield <nathan at code.databio.org>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("LOLA")

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("LOLA")

 

HTML	R Script	1. Getting Started with LOLA
HTML	R Script	2. Using LOLA Core
HTML	R Script	3. Choosing a Universe
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, MethylSeq, Sequencing, Software, SystemsBiology
Version	1.26.0
In Bioconductor since	BioC 3.2 (R-3.2) (7 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods
LinkingTo
Suggests	parallel, testthat, knitr, BiocStyle, rmarkdown
SystemRequirements
Enhances	simpleCache, qvalue, ggplot2
URL	http://code.databio.org/LOLA
BugReports	http://github.com/nsheff/LOLA
Depends On Me
Imports Me
Suggests Me	COCOA, DeepBlueR, MAGAR, MIRA, ramr
Links To Me
Build Report

Package Archives

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

Source Package	LOLA_1.26.0.tar.gz
Windows Binary	LOLA_1.26.0.zip
macOS Binary (x86_64)	LOLA_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LOLA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LOLA
Package Short Url	https://bioconductor.org/packages/LOLA/
Package Downloads Report	Download Stats