Man pages for neurogenomics/orthogene
Interspecies gene mapping
| add_synonyms | Add gene synonyms |
| aggregate_mapped_genes | Aggregate/expand a gene matrix by gene mappings |
| aggregate_rows | Aggregate rows of matrix |
| aggregate_rows_monocle3 | Aggregate rows: monocle3 |
| all_genes | Get all genes |
| all_genes_babelgene | Get all genes: babelgene |
| all_species | All species |
| check_gene_df_type | Check gene_df |
| convert_orthologs | Map genes from one species to another |
| create_background | Create gene background |
| dMcast | dMcast |
| earthworm2human_map | Earthworm to human map |
| exp_mouse | Gene expression data: mouse |
| exp_mouse_enst | Transcript expression data: mouse |
| format_species | Format species names |
| get_orgdb_genomeinfodbdata | Import organism database: GenomeInfoDbData |
| get_silhouettes | Get silhouettes |
| ggtree_plot | Plot a phylogenetic tree |
| gprofiler_namespace | gconvert namespaces |
| gprofiler_orgs | Reference organisms |
| infer_species | Infer species from gene names |
| infer_species_plot | infer_species_plot |
| invert_dictionary | Invert dictionary |
| many2many_rows | Expand/aggregate rows of matrix for many:many mappings |
| map_genes | Map genes |
| map_genes_planosphere | Map genes: SMED |
| map_orthologs | Map orthologs |
| map_orthologs_babelgene | Map orthologs: babelgene |
| map_orthologs_custom | Map orthologs: gprofiler |
| map_orthologs_gprofiler | Map orthologs: gprofiler |
| map_orthologs_homologene | Map orthologs: homologene |
| map_species | Standardise species names |
| message_parallel | Send messages to console even from within parallel processes |
| orthogene-package | 'orthogene': Interspecies gene mapping |
| plot_benchmark_bar | Plot benchmark: bar |
| plot_benchmark_scatter | Plot benchmark: scatter |
| plot_orthotree | Create a phylogenetic tree of shared orthologs |
| prepare_tree | Prepare a phylogenetic tree |
| remove_image_bg | Remove image background |
| report_orthologs | Report orthologs |
| run_benchmark | Run benchmark tests |
| set_gprofiler | Set gprofiler |
| taxa_id_dict | Taxa ID dictionary |
