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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 (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews Coverage, DataImport, GenomeAssembly, Sequencing, Software, WorkflowStep
Version 1.1.0
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
System Requirements
URL https://github.com/nahid18/easylift https://nahid18.github.io/easylift
Bug Reports https://github.com/nahid18/easylift/issues
See More
Suggests testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package easylift_1.1.0.tar.gz
Windows Binary easylift_1.1.0.zip
macOS Binary (x86_64) easylift_1.1.0.tgz
macOS Binary (arm64) easylift_1.1.0.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