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AllPairwiseAlign()
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Compute all pairwise (global) alignments with VSEARCH |
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CLUSTpred()
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Cluster Sequences with VSEARCH |
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LTRdigest()
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Run LTRdigest to predict putative LTR Retrotransposons |
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LTRharvest()
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Run LTRharvest to predict putative LTR Retrotransposons |
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LTRpred()
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Predict LTR retrotransposons in a given genome |
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LTRpred.meta()
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Perform Meta-Analyses with LTRpred |
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ORFpred()
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Open Reading Frame Prediction |
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SimMatAbundance()
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Compute histogram shape similarity between species |
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assign.short.sci.name()
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Transform long file names to short scientific names |
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bcolor()
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Colors scheme for plots |
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clust2fasta()
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Export sequences of TEs belonging to the same cluster |
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cluster.members()
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Select members of a specific cluster |
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cn2bed()
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Write copy number estimation results to BED file format. |
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combinePreds()
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Combine LTRpred prediction files |
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dfam.query()
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Query the Dfam database to annotate putative LTRs |
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file.move()
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Move folders from one location to another |
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filter.jumpers()
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Detect LTR retrotransposons that are potential jumpers |
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filter.uc()
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Filter for cluster members |
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generate.multi.quality.filter.meta()
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Run quality.filter.meta for several different ltr similarity thresholds. |
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genome.summary()
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Generating genome summary files for LTRpred.meta results |
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get.pred.filenames()
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Retrieve file names of files genereated by LTRpred |
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get.seqs()
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Quickly retrieve the sequences of a Biostrings object |
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gridPlotAssemblyVersions()
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Plot retrotransposon age distributions for predictions of different genome assembly versions |
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join.with.genome.tbl()
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Join gm_files returned by generate.multi.quality.filter.meta with a genome information table |
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ltr.cn()
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Copy Number Quantification of predicted LTRs (solo LTR prediction) |
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ltr_age_estimation()
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Estimate retrotransposon insertion age in Mya based on 5 prime and 3 prime LTR sequence homology |
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meta.apply()
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Apply functions to meta data generated by LTRpred |
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meta.seq.space()
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Quantification of the repeat space for multiple Repeat Masker files |
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meta.summarize()
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Summarize (concatenate) all predictions of a LTRpred.meta run |
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motif.count()
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Low level function to detect motifs in strings |
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plotLTRSim()
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Plot the age distribution of predicted LTR transposons |
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plot_element_distr_along_chromosome()
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Plot positions of predicted retrotransposons along chromosomes |
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pred2GRanges()
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Format LTR prediction data to GRages object |
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pred2bed()
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Format LTR prediction data to BED file format |
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pred2csv()
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Format LTR prediction data to CSV file format |
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pred2fasta()
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Save the sequence of the predicted LTR Transposons in a fasta file |
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pred2gff()
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Format LTR prediction data to GFF3 file format |
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pred2orfseqs()
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Save the ORF sequence of the predicted LTR Transposons in a fasta file |
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pred2tsv()
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Format LTR prediction data to TSV file format |
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quality.filter()
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Pipeline to eliminate false positive predictions of retrotransposons |
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quality.filter.meta()
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Pipeline to eliminate false positive predictions of retrotransposons at a metagenomic scale |
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quant.cds.space()
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Quantify the coding sequence space within a genome |
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quant.protein.space()
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Quantify the protein space within a genome |
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quant.repeat.space()
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Quantify the repeat space within a genome |
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quant.space.meta()
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Quantify the genomic loci space for multiple genomes, proteomes or Repeat Masker annotation files |
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read.blast6out()
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Read file in blast6out format generated by USEARCH or VSEARCH |
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read.dfam()
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Import Dfam Query Output |
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read.ltrpred()
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Import LTRpred DataSheet |
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read.orfs()
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Read output of ORFpred |
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read.prediction()
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Import the output of LTRharvest or LTRdigest |
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read.seqs()
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Import sequences of predicted LTR transposons |
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read.tabout()
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Import information sheet returned by LTRdigest |
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read.uc()
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Read file in USEARCH cluster format |
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rename.fasta()
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Helper function to add species names to headers within fasta files |
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rename.fasta.meta()
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Meta function for applying rename.fasta |
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rename.organisms()
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Rename file path names from read_proteome, etc. |
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repbase.clean()
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Clean the initial Repbase database for BLAST |
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repbase.filter()
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Filter the Repbase query output |
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repbase.query()
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Query the RepBase to annotate putative LTRs |
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tidy.datasheet()
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Select most important columns of LTRpred output for further analytics |
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totalRepeatSpace()
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Quantify the total repeat space from Repeat Masker output in Mbp |
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ws.wrap.path()
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Wrap whitespace in paths |