Man pages for arendsee/synder
Use Synteny to Filter Genomic Search
| anon_search | Wrapper for search allowing simple interval inputs |
| as_conlen | Convert to a contig length (Seqinfo) object |
| as_gff | Convert to a synder GFF object |
| as_synmap | Convert to a synder Synmap object |
| c_count | count overlaps |
| c_dump | print all blocks with contiguous set ids |
| c_filter | remove links that disagree with the synteny map |
| c_map | trace intervals across genomes |
| c_search | predict search intervals |
| dot-overlaps | Join two tables by overlapping rows |
| featureMap | Map features between GFFs based on a synder SearchResult |
| flag_summary | Summarize the flags returned from a search |
| intro_1 | Intro vignette dataset 1 |
| intro_2 | Intro vignette dataset 2 |
| is_incoherent | Determine which search intervals are not in well-behaved... |
| is_unassembled | Determine which queries map off the ends of a scaffold |
| load_blastp_file | Load a protein BLAST file |
| load_tblastn_file | Load a tBLASTn file |
| make_blastp_map | Map intervals for protein blast |
| make_tblastn_gene_map | make gene map |
| make_tblastn_si_map | tBLASTn search interval map |
| neighborhood_madness | Calculate the local scrambledness in the region around each... |
| plot.DumpResult | Print the result of dumping a synteny map |
| plot.SearchResult | Plot the result of a search operations |
| plot.Synmap | Plot a synteny map |
| synder | synder: Trace intervals between genomes |
| synder_cast | Synder cast functions |
| synder_classes | Synder classes |
| synder_commands | Synder Commands |
| synder_print | Synder print functions |
| synder_read | Synder read functions |
| syntenic_density | Calculate a metric for the overall density of the synteny map |
| syntenic_scatter | Calculate a metric for the overall scrambledness of the... |
| toy | Toy dataset for synder |
| ty1 | Yeast Ty1 mobile genetic element dataset |
