Package: easylift 1.5.0

Abdullah Al Nahid

easylift: An R package to perform genomic liftover

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.

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

easylift_1.5.0.tar.gz
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easylift.pdf |easylift.html
easylift/json (API)
NEWS

# Install 'easylift' in R:
install.packages('easylift', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nahid18/easylift/issues

Pkgdown site:https://nahid18.github.io

On BioConductor:easylift-1.5.0(bioc 3.21)easylift-1.4.0(bioc 3.20)

softwareworkflowstepsequencingcoveragegenomeassemblydataimport

5.00 score 5 stars 7 scripts 182 downloads 1 exports 82 dependencies

Last updated 5 months agofrom:16c9c5bed1. Checks:3 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 28 2025
R-4.5-winNOTEFeb 28 2025
R-4.5-macNOTEFeb 28 2025
R-4.5-linuxNOTEFeb 28 2025
R-4.4-winNOTEFeb 28 2025
R-4.4-macNOTEFeb 28 2025
R-4.3-winOKFeb 28 2025
R-4.3-macOKFeb 28 2025

Exports:easylift

Dependencies:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpurrrR.methodsS3R.ooR.utilsR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLXVectoryaml

Perform Genomic Liftover

Rendered fromeasylift.Rmdusingknitr::rmarkdownon Feb 28 2025.

Last update: 2023-10-24
Started: 2023-08-25