LOLA
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see LOLA.
Locus overlap analysis for enrichment of genomic ranges
Bioconductor version: 3.9
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("LOLA")):
Installation
To install this package, start R (version "3.6") 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")| 1. Getting Started with LOLA | HTML | R Script |
| 2. Using LOLA Core | HTML | R Script |
| 3. Choosing a Universe | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, MethylSeq, Sequencing, Software, SystemsBiology |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.10) |
| 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 |
See More
| Suggests | parallel, testthat, knitr, BiocStyle, rmarkdown |
| Linking To | |
| Enhances | simpleCache, qvalue, ggplot2 |
| Depends On Me | |
| Imports Me | |
| Suggests Me | COCOA, DeepBlueR, MIRA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | LOLA_1.14.0.tar.gz |
| Windows Binary | LOLA_1.14.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | LOLA_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/LOLA |
| Source Repository (Developer Access) | git clone [email protected]:packages/LOLA |
| Bioc Package Browser | https://code.bioconductor.org/browse/LOLA/ |
| Package Short Url | https://bioconductor.org/packages/LOLA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |