easylift

The goal of easylift is to perform genomic liftover given GRanges and chain file.

Installation

Get the latest development version from GitHub with:

BiocManager::install("nahid18/easylift")

Usage

First, import the libraries

library("easylift")
library("GenomicRanges")

Then, execute the code below. This assumes you already downloaded the required chain file.

gr <- GRanges(seqname = Rle(paste("chr", 1, sep = "")),
              ranges = IRanges(start = 1, end = 200000))
genome(gr) <- "hg19"
to <- "hg38"
chain <- "hg19ToHg38.over.chain.gz"
lifted <- easylift(gr, to, chain)

Citation

To cite package ‘easylift’ in publications use:

Al Nahid A, Love M (2023). easylift: An R package to perform genomic liftOver. R package version 0.0.1, https://github.com/nahid18/easylift.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {easylift: An R package to perform genomic liftOver},
    author = {Abdullah {Al Nahid} and Michael Love},
    year = {2023},
    note = {R package version 0.0.1},
    url = {https://github.com/nahid18/easylift},
  }

Please note that the easylift was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the easylift project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.