liftOver

DOI: 10.18129/B9.bioc.liftOver    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see liftOver.

Changing genomic coordinate systems with rtracklayer::liftOver

Bioconductor version: 3.9

The liftOver facilities developed in conjunction with the UCSC browser track infrastructure are available for transforming data in GRanges formats. This is illustrated here with an image of the EBI/NHGRI GWAS catalog that is, as of May 10 2017, distributed with coordinates defined by NCBI build hg38.

Author: Bioconductor Package Maintainer [aut, cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("liftOver")

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("liftOver")

 

HTML

R Script

Changing genomic coordinate systems with rtracklayer::liftOver

Details

biocViews	BasicWorkflow, Workflow
Version	1.8.0
License	Artistic-2.0
Depends	R (>= 3.3.0), gwascat, GenomicRanges, rtracklayer, Homo.sapiens, BiocGenerics
Imports
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://www.bioconductor.org/help/workflows/liftOver/
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package	liftOver_1.8.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/liftOver
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/liftOver
Package Short Url	https://bioconductor.org/packages/liftOver/
Package Downloads Report	Download Stats