Package: packFinder 1.17.0
Jack Gisby
packFinder: de novo Annotation of Pack-TYPE Transposable Elements
Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).
Authors:
packFinder_1.17.0.tar.gz
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packFinder.pdf |packFinder.html✨
packFinder/json (API)
NEWS
| # Install 'packFinder' in R: |
| install.packages('packFinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jackgisby/packfinder/issues
- arabidopsisThalianaRefseq - Arabidopsis thaliana Refseq Genome Chromosome 3 Subset
- packMatches - Sample packFinder Output
On BioConductor:packFinder-1.17.0(bioc 3.20)packFinder-1.16.0(bioc 3.19)
Last updated 2 months agofrom:639edef741
Exports:blastAnalysisblastAnnotatecollapseSeqsfilterWildcardsgetPackSeqsgetPacksFromCsvgetPacksFromFastagetPacksFromGRangesgetTsdsidentifyPotentialPackElementsidentifyTirMatchesmakeBlastDbpackAlignpackBlastpackClustpackSearchpacksToCsvpacksToFastapacksToGRangesreadBlastreadUctirClust
Dependencies:apeaskpassBiocGenericsBiostringscrayoncurldigestGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitekmerlatticemimenlmeopensslphylogramR6RcppS4VectorssysUCSC.utilsXVectorzlibbioc
