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LOLA

Locus overlap analysis for enrichment of genomic ranges

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("LOLA")):

Installation

To install this package, start R (version "4.3") 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")
1. Getting Started with LOLA HTML R Script
2. Using LOLA Core HTML R Script
3. Choosing a Universe HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, MethylSeq, Sequencing, Software, SystemsBiology
Version 1.30.0
In Bioconductor since BioC 3.2 (R-3.2) (8 years)
License GPL-3
Depends R (>= 3.5.0)
Imports BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods
Linking To
Suggests parallel, testthat, knitr, BiocStyle, rmarkdown
System Requirements
Enhances simpleCache, qvalue, ggplot2
URL http://code.databio.org/LOLA
Bug Reports http://github.com/nsheff/LOLA
See More
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_1.30.0.tar.gz
Windows Binary LOLA_1.30.0.zip (64-bit only)
macOS Binary (x86_64) LOLA_1.30.0.tgz
macOS Binary (arm64) LOLA_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/LOLA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/LOLA
Bioc Package Browser https://code.bioconductor.org/browse/LOLA/
Package Short Url https://bioconductor.org/packages/LOLA/
Package Downloads Report Download Stats