Package: packFinder 1.19.0
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_1.19.0.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-1.19.0(bioc 3.21)packFinder-1.18.0(bioc 3.20)
geneticssequencematchingannotationbioinformaticstext-mining
Last updated 4 months agofrom:7ce40932f6. Checks:3 OK, 5 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 03 2025 |
| R-4.5-win | NOTE | Feb 03 2025 |
| R-4.5-mac | NOTE | Feb 03 2025 |
| R-4.5-linux | NOTE | Feb 03 2025 |
| R-4.4-win | NOTE | Feb 03 2025 |
| R-4.4-mac | NOTE | Feb 03 2025 |
| R-4.3-win | OK | Feb 03 2025 |
| R-4.3-mac | OK | Feb 03 2025 |
Exports:blastAnalysisblastAnnotatecollapseSeqsfilterWildcardsgetPackSeqsgetPacksFromCsvgetPacksFromFastagetPacksFromGRangesgetTsdsidentifyPotentialPackElementsidentifyTirMatchesmakeBlastDbpackAlignpackBlastpackClustpackSearchpacksToCsvpacksToFastapacksToGRangesreadBlastreadUctirClust
Dependencies:apeaskpassBiocGenericsBiostringscrayoncurldigestgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitekmerlatticemimenlmeopensslphylogramR6RcppS4VectorssysUCSC.utilsXVector
