LOLA

This is the released version of LOLA; for the devel version, see LOLA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

Locus overlap analysis for enrichment of genomic ranges

Bioconductor version: Release (3.23)

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")):

Nathan Sheffield. LOLA: Locus overlap analysis for enrichment of genomic ranges. doi:10.18129/B9.bioc.LOLA, R package version 1.42.0, https://bioconductor.org/packages/LOLA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, MethylSeq, Sequencing, Software, SystemsBiology
Version	1.42.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods
System Requirements
URL	http://code.databio.org/LOLA
Bug Reports	http://github.com/nsheff/LOLA

Suggests	parallel, XVector, testthat, knitr, BiocStyle, rmarkdown
Linking To
Enhances	simpleCache, qvalue, ggplot2
Depends On Me
Imports Me
Suggests Me	COCOA, MAGAR, MIRA, ramr
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	LOLA_1.42.0.tar.gz
Windows Binary (x86_64)	LOLA_1.42.0.zip
macOS Binary (big-sur-x86_64)	LOLA_1.42.0.tgz
macOS Binary (sonoma-arm64)	LOLA_1.42.0.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