Man pages for almeidasilvaf/syntenet
Inference And Analysis Of Synteny Networks
| angiosperm_phylogeny | Microsynteny-based angiosperm phylogeny. |
| annotation | Filtered genome annotation for Ostreococcus sp. species |
| binarize_and_transpose | Binarize and transpose the phylogenomic profile matrix |
| blast_list | List of data frames containing BLAST-like tabular output |
| check_input | Check if input objects are ready for further analyses |
| cluster_network | Cluster the synteny network using the Infomap algorithm |
| clusters | Synteny network clusters of BUSCO genes for 25 eudicot... |
| collapse_protein_ids | Collapse protein IDs into gene IDs in sequence names of... |
| create_species_id_table | Create a data frame of species IDs (3-5-character... |
| diamond_is_installed | Check if DIAMOND is installed |
| edges | Synteny network of Ostreococcus genomes represented as an... |
| export_sequences | Export processed sequences as FASTA files |
| fasta2AAStringSetlist | Read FASTA files in a directory as a list of AAStringSet... |
| find_GS_clusters | Find group-specific clusters based on user-defined species... |
| gff2GRangesList | Read GFF/GTF files in a directory as a GRangesList object |
| infer_microsynteny_phylogeny | Infer microsynteny-based phylogeny with IQTREE |
| infer_syntenet | Infer synteny network |
| interspecies_synteny | Detect interspecies synteny |
| intraspecies_synteny | Detect intraspecies synteny |
| iqtree_is_installed | Check if IQTREE is installed |
| iqtree_version | Get IQ-TREE version |
| last_is_installed | Check if last is installed |
| network | Synteny network of BUSCO genes for 25 eudicot species |
| parse_collinearity | Parse .collinearity files obtained with MCScan |
| phylogenomic_profile | Perform phylogenomic profiling for synteny network clusters |
| plot_network | Plot network |
| plot_profiles | Plot a heatmap of phylogenomic profiles |
| process_input | Process sequence data |
| profiles2phylip | Save the transposed binary profiles matrix to a file in... |
| proteomes | Filtered proteomes of Ostreococcus sp. species |
| rcpp_mcscanx_file | rcpp_mcscanx_file |
| read_diamond | Read DIAMOND/BLAST tables as a list of data frames |
| run_diamond | Wrapper to run DIAMOND from an R session |
| run_last | Wrapper to run last from an R session |
| scerevisiae_annot | Genome annotation of the yeast species S. cerevisiae |
| scerevisiae_diamond | Intraspecies DIAMOND output for S. cerevisiae |
| syntenet-package | syntenet: Inference And Analysis Of Synteny Networks |
