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
