# de novo Annotation of Pack-TYPE Transposable Elements

## Documentation for package ‘packFinder’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

arabidopsisThalianaRefseq | Arabidopsis thaliana Refseq Genome Chromosome 3 Subset
blastAnalysis | BLAST Analysis of PackTYPE Elements
blastAnnotate | Functional Annotation of PackTYPE Elements
collapseSeqs | Collapse Overlapping Sequences
filterWildcards | Remove Low Quality Sequences
getPackSeqs | Extract Sequences of Pack-TYPE Elements
getPacksFromCsv | Retrieve Saved packFinder Results (.csv)
getPacksFromFasta | Retrieve Saved packFinder Results (.fasta)
getPacksFromGRanges | Retrieve packFinder Results from GRanges Object
getTsds | Get Flanking Terminal Site Duplication Sequences
identifyPotentialPackElements | Pack Element Filtering
identifyTirMatches | Identify Terminal Inverted Repeat Matches
makeBlastDb | Make Blast Database
packAlign | Global Alignment with VSEARCH
packBlast | Pipeline for BLAST/Classification of PackTYPE Elements
packClust | Cluster Transposons with VSEARCH
packFinder | packFinder: a package for the de novo Annotation of Pack-TYPE Transposable Elements
packMatches | Sample packFinder Output
packSearch | packFinder Algorithm Pipeline
packsToCsv | Save packFinder Results in CSV Format (.csv)
packsToFasta | Save packFinder Results in FASTA Format (.fasta)
packsToGRanges | Export packFinder Results to a GRanges Object
readBlast | Convert NCBI BLAST+ Files to Dataframe
readUc | Convert .uc Files to Dataframe
tirClust | Analyse TIR Sequences of Pre-clustered Transposable Elements