Man pages for irycisBioinfo/PATO
Pangenome Analysis Toolkit
| accnet | Build accessory genome network (AccNET) |
| accnet_enrichment_analysis | Enrichment analysis of accessory genome |
| accnet_with_padj | Creates a AccNET network using the enrichment analysis |
| annotate | Annotate Virulence Factors and Antibiotic Resistance Genes |
| as.data.frame.nr_list | Wrapper to change format between nr_list and data.frame |
| classifier | Classifier |
| cluster_accnet | Internal function to cluster accnet data |
| cluster_files_from_distance | Internal Function of the workflow pangenomes_from_file |
| clustering | Clustering genomes |
| cluster_knnn | Internal function to cluster igraph data |
| cluster_mash | Internal function to cluster mash data |
| coincidents | Find coincidents gene/proteins (clustering) |
| core_genome | Core-Genome Alignment |
| core_plots | Plot the size of core-genome, accessory-genome and pan-genome |
| core_snp_genome | Core SNP Genome |
| core_snps_matrix | Core SNPs matrix |
| dn_ds | dN/dS Average Ratio This function perform the dN/dS ratios... |
| eggnogmapper | EggNogg Mapper |
| export_accnet_aln | Export accesory genome binary multi-alignment. |
| export_core_to_fasta | Export core-genome alignment to Multi-alignment FASTA file. |
| export_to_gephi | Export accnet or igraph object to GraphML format |
| extract_non_redundant | Create a accnet or mash object with the representatives... |
| heatmap_of_annotation | HeatMap of Annotation (VF and/or AbR) |
| install_db | Install PATO reference data bases |
| knnn | K-Nearest Neighbour Network |
| load_gff_list | Load GFF3 file list |
| mash | MASH distance estimation. |
| mmseqs | MMSeqs2 Orthologous clustering. |
| network_of_annotation | Network of Annotation |
| non_redundant | Non Redundant set of samples. |
| non_redundant_hier | Non Redundant set of samples using hierarchical search. |
| non_redundant_pangenomes | Non redundant pangenomes. |
| outliers | Find outliers in the dataset. |
| pangenomes_from_files | Creates Pangenomes from file list |
| pangenomes_from_files_mmseqs | Individual pangenome clustering from file-list |
| pangenomes_from_mmseqs | Creates Pangenomes from mmseqs object |
| pangenomes_mmseqs | Final step of pangenomes homologous cluster |
| plasmidome | Plasmidome: Extract the plasmid sequences from a set of... |
| plot_knnn_network | Plot K-Nearest Neighbour Network |
| remove_outliers | Remove the outliers of a data set (mash or accnet) |
| screening | Screening genes markers |
| sharedness | Creates a matrix of sharedness |
| similarity_network | Similarity Network |
| similarity_tree | Similarity tree |
| singles | Find singles (genes/proteins) in a AccNET object |
| snps_map | SNPs Map |
| snps_pairwaise | Direct SNPs pairwaise. |
| twins | Finds Twins into AccNET object |
| umap_plot | Plot UMAP representation of a data set. |
