de novo Annotation of Pack-TYPE Transposable Elements

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Documentation for package ‘packFinder’ version 1.20.0

• 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