Man pages for packFinder
de novo Annotation of Pack-TYPE Transposable Elements

arabidopsisThalianaRefseqArabidopsis thaliana Refseq Genome Chromosome 3 Subset
blastAnalysisBLAST Analysis of PackTYPE Elements
blastAnnotateFunctional Annotation of PackTYPE Elements
collapseSeqsCollapse Overlapping Sequences
filterWildcardsRemove Low Quality Sequences
getPackSeqsExtract Sequences of Pack-TYPE Elements
getPacksFromCsvRetrieve Saved packFinder Results (.csv)
getPacksFromFastaRetrieve Saved packFinder Results (.fasta)
getPacksFromGRangesRetrieve packFinder Results from GRanges Object
getTsdsGet Flanking Terminal Site Duplication Sequences
identifyPotentialPackElementsPack Element Filtering
identifyTirMatchesIdentify Terminal Inverted Repeat Matches
makeBlastDbMake Blast Database
packAlignGlobal Alignment with VSEARCH
packBlastPipeline for BLAST/Classification of PackTYPE Elements
packClustCluster Transposons with VSEARCH
packFinderpackFinder: a package for the de novo Annotation of Pack-TYPE...
packMatchesSample packFinder Output
packSearchpackFinder Algorithm Pipeline
packsToCsvSave packFinder Results in CSV Format (.csv)
packsToFastaSave packFinder Results in FASTA Format (.fasta)
packsToGRangesExport packFinder Results to a GRanges Object
readBlastConvert NCBI BLAST+ Files to Dataframe
readUcConvert .uc Files to Dataframe
tirClustAnalyse TIR Sequences of Pre-clustered Transposable Elements
packFinder documentation built on Nov. 8, 2020, 5:24 p.m.