easylift
An R package to perform genomic liftover
Bioconductor version: Release (3.20)
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("easylift")):
Installation
To install this package, start R (version "4.4") 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")| Perform Genomic Liftover | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, DataImport, GenomeAssembly, Sequencing, Software, WorkflowStep |
| Version | 1.4.0 |
| 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 |
See More
| 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_1.4.0.tar.gz |
| Windows Binary (x86_64) | easylift_1.4.0.zip |
| macOS Binary (x86_64) | easylift_1.4.0.tgz |
| macOS Binary (arm64) | easylift_1.3.0.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 |