Man pages for jackgisby/packFinder
de novo Annotation of Pack-TYPE Transposable Elements
| 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... |
| 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 |
