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'))

Peer review:

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 115 downloads 1 exports 83 dependencies

Last updated 3 months agofrom:16c9c5bed1. Checks:3 OK, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKDec 30 2024
R-4.5-winNOTEDec 31 2024
R-4.5-linuxNOTEDec 30 2024
R-4.4-winNOTEDec 31 2024
R-4.4-macNOTEDec 30 2024
R-4.3-winOKNov 30 2024
R-4.3-macOKDec 30 2024

Exports:easylift

Dependencies:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpurrrR.methodsS3R.ooR.utilsR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLXVectoryamlzlibbioc

Perform Genomic Liftover

Rendered fromeasylift.Rmdusingknitr::rmarkdownon Dec 30 2024.

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