To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LOLA")
In most cases, you don't need to download the package archive at all.
LOLA
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see LOLA.
Location overlap analysis for enrichment of genomic ranges
Bioconductor version: 3.3
Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This make is 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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LOLA")
Documentation
| HTML | R Script | Choosing a LOLA Universe |
| HTML | R Script | Getting Started with LOLA |
| HTML | R Script | Using LOLA Core |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, MethylSeq, Sequencing, Software, SystemsBiology |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1 year) |
| License | GPL-3 |
| Depends | |
| Imports | BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table |
| LinkingTo | |
| Suggests | knitr, parallel, testthat |
| SystemRequirements | |
| Enhances | simpleCache, qvalue |
| URL | http://databio.org/lola |
| BugReports | http://github.com/sheffien/LOLA |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | LOLA_1.2.2.tar.gz |
| Windows Binary | LOLA_1.2.2.zip |
| Mac OS X 10.9 (Mavericks) | LOLA_1.2.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/LOLA/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/LOLA/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
