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