easylift

DOI: 10.18129/B9.bioc.easylift  

An R package to perform genomic liftover

Bioconductor version: Release (3.18)

The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor's GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.

Author: Abdullah Al Nahid [aut, cre] , Hervé Pagès [aut, rev], Michael Love [aut, rev]

Maintainer: Abdullah Al Nahid <abdnahid56 at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("easylift")

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("easylift")

 

HTML	R Script	Perform Genomic Liftover
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Coverage, DataImport, GenomeAssembly, Sequencing, Software, WorkflowStep
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	GenomicRanges, BiocFileCache
Imports	rtracklayer, GenomeInfoDb, R.utils, tools, methods
LinkingTo
Suggests	testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/nahid18/easylift https://nahid18.github.io/easylift
BugReports	https://github.com/nahid18/easylift/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	easylift_1.0.0.tar.gz
Windows Binary	easylift_1.0.0.zip
macOS Binary (x86_64)	easylift_1.0.0.tgz
macOS Binary (arm64)	easylift_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/easylift
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/easylift
Bioc Package Browser	https://code.bioconductor.org/browse/easylift/
Package Short Url	https://bioconductor.org/packages/easylift/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive