easylift

This is the development version of easylift; for the stable release version, see easylift.

An R package to perform genomic liftover

Bioconductor version: Development (3.21)

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] (ORCID: ), Hervé Pagès [aut, rev], Michael Love [aut, rev] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DataImport, GenomeAssembly, Sequencing, Software, WorkflowStep
Version	1.5.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
License	MIT + file LICENSE
Depends	GenomicRanges, BiocFileCache
Imports	rtracklayer, GenomeInfoDb, R.utils, tools, methods
System Requirements
URL	https://github.com/nahid18/easylift https://nahid18.github.io/easylift
Bug Reports	https://github.com/nahid18/easylift/issues

Suggests	testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	easylift_1.5.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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