LOLA

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see LOLA.

Locus overlap analysis for enrichment of genomic ranges

Bioconductor version: 3.6

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 [cre]

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

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

Installation

To install this package, start R (version "3.4") 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


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	1.8.0
In Bioconductor since	BioC 3.2 (R-3.2) (8.5 years)
License	GPL-3
Depends
Imports	BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats
System Requirements
URL	http://databio.org/lola
Bug Reports	http://github.com/nsheff/LOLA

Suggests	knitr, parallel, testthat, BiocStyle, rmarkdown
Linking To
Enhances	simpleCache, qvalue, ggplot2
Depends On Me
Imports Me
Suggests Me	DeepBlueR
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	LOLA_1.8.0.tar.gz
Windows Binary	LOLA_1.8.0.zip
Mac OS X 10.11 (El Capitan)	LOLA_1.8.0.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
Old Source Packages for BioC 3.6	Source Archive