Man pages for frankkramer-lab/Multipath
Pathway Data Integration With Influencing Knowledge Using Multi-Layered Graphs
| addDBLayer | Add a drug layer to a mully graph |
| addDiseaseLayer | Add OMIM Layer with its respective Nodes |
| addGenesLayer | Add KEGG Gene Layer with its respective Nodes |
| addStep | Track a modification of a graph |
| addUPKBLayer | Add a protein layer to a mully graph |
| downloadPathway | Download Reactome Pathways in BioPAX level 2 and 3 |
| filterGeneList | Remove invalid Gene IDs from a gene list |
| getDBCarriers | Get the carrier proteins involved in movement of given drugs... |
| getDBDrug | Get DrugBank drug entry |
| getDBDrugInteractions | Get DrugBank Drug to Drug Interactions |
| getDBEnzymes | Get the enzymes inhibited/induced or involved in metabolism... |
| getDBTargets | Get the targets of given DrugBank drugs |
| getDBtoUPKB | Get DrugBank Drugs to UniProt Proteins Relations from... |
| getDBTransporters | Get the transporter proteins involved in movement of given... |
| getExternalIDs | Get External Database IDs of nodes |
| getInternalIDs | Get Internal ID of a given node or list of nodes |
| getKeggGene | Get Kegg gene |
| getKeggOmimRelation | Gets the genes and diseases that are referenced to each... |
| getKEGGtoDATABASE | Get KEGG Genes to a Database cross-reference from KEGG |
| getKEGGtoOMIM | Get KEGG Genes to Omim relations from KEGG |
| getKeggUpkbRelations | Gets the genes and proteins that are referenced to each other |
| getOmimToKEGG | Get Omim to KEGG Genes relations from OMIM |
| getOmimToUPKB | Get Omim to UPKB relations from OMIM |
| getPathwayID | Get internal pathway ID in a BioPAX file |
| getRelatedGenes | Get proteins that has a reference to KEGG Genes from a mully... |
| getUPKBDBRelations | Get Protein and Drugs relations from UniProt and DrugBank |
| getUPKBInfo | Get Proteins from UniProtKB |
| getUPKBInteractions | Get the interactions of given proteins from UniProt |
| getUPKBRelatedDiseases | Get proteins that has a reference to OMIM from a mully graph... |
| getUPKBtoDB | Get UniProt Proteins to DrugBank Drugs relations from UniProt |
| getUPKBtoKEGG | Get UniProt Proteins to KEGG Genes relations from UPKB |
| interactionKegg | Interaction between KEGG genes and other databases |
| is_valid_kegg_gene | Check KEGG Gene Code Validity |
| loadDBXML | Load DrugBank XML file |
| multipath | Generate Multipath Graph from General Data |
| pathway2Mully | Build a mully graph from a given pathway |
| pathwayView | Create an empty view |
| print.pathwayView | Print function |
| simplifyInteractionKegg | Simplify the dataframe's structure |
| transformKeggData | Transform data retrieved from KEGG |
| undo | Undo a modification step in a view |
| wntpathway | Demo function for Wnt Pathway Views |
