Man pages for jtlovell/GENESPACE
Synteny- and orthology-constrained comparative genomics
| annotate_bed | Combine and annotate bed files |
| annotate_blast | Combine and annotate blast files |
| classify_genome | classify the genome based on bed coordinates |
| clean_windows | Syntenic windowed whole-genome alignments |
| convert_input2v1 | Convert input data formats |
| find_contigsGapsTelos | get coordinates aggregated across kmers |
| find_kmers | Generic internal functions used by genespace |
| gviz_utils | Generic internal functions used by genespace |
| init_genespace | Find files and directories for a GENESPACE run |
| integrate_synteny | Integrate syntenic positions across multiple genomes |
| parse_annotations | Accessory function to help build GENESPACE input files |
| plot_2genomes | Comparative genome structure plots |
| plot_contigs | Plot contigs, gaps and telomeres |
| plot_hits | plot hits as a xy dotplot |
| plot_riparian | Make riparian plot using hits, not OGs |
| query_genespace | Query GENESPACE results |
| run_genespace | The GENESPACE pipeline |
| run_mcscanx | run_mcscanx |
| run_orthofinder | Accessory function to run OrthoFinder |
| set_syntenyParams | Set synteny parameters and parse required data |
| slide_genome | sliding window on a list of granges |
| syntenic_orthogroups | construct syntenic orthogroups from pairwise blast |
| syntenic_pangenes | generate syntenic pan-gene sets |
| synteny | flag and split syntenic hits |
| utils | Generic internal functions used by genespace |
