Man pages for lptolik/synaptome.db
Synamptosome Proteome Database
| dot-getdbfile | Hidden function that creates a local copy of the database. |
| dot-onLoad | Hidden load function. Check the presence of the database and... |
| findGeneByCompartmentPaperCnt | Get gene table of frequently found genes within compartments |
| findGeneByPaperCnt | Get gene table of frequently found genes |
| findGeneByPapers | Get gene table of frequently found genes |
| findGenesByEntrez | Internal Gene representation for given list of gene Entrez... |
| findGenesByName | Find GeneIDs for names |
| getAllGenes4BrainRegion | Get all genes for brain region for particular specie |
| getAllGenes4Compartment | Extract all genes found in compartment |
| getBrainRegions | Get list of all Brain regions in the database |
| getCompartments | Get full list of compartments |
| get_dbconn | Get dbcon. Return connection to the database. |
| getGeneDiseaseByEntres | Disease information for Human Entrez IDs |
| getGeneDiseaseByIDs | Disease information for internal gene IDs. |
| getGeneDiseaseByName | Disease information for Human Gene Names |
| getGeneDiseaseQuery | Prepare query for Disease table |
| getGeneIdByCompartmentPaperCnt | Get list of frequently found in 'Compartment GeneIDs |
| getGeneIdByEntrez | Get list of GeneIDs corresponding to provided Entrez IDs. |
| getGeneIdByName | Get list of GeneIDs corresponding to provided gene names. |
| getGeneIdByPaperCnt | Get list of frequently found GeneIDs |
| getGeneIdByPapers | Get list of GeneIDs for genes found in specified papers |
| getGeneInfoByEntrez | Gene information for given list of gene Entrez IDs |
| getGeneInfoByIDs | Get GeneInfo table for set of GeneIDs |
| getGeneInfoByName | Get gene information for set of gene names. |
| getGeneInfoByPapers | Get gene information for set of genes mentioned by certain... |
| getGenes4BrainRegion | Select genes from the list that found in brain region of... |
| getGenes4Compartment | Select genes from the list that found in compartment |
| getGenesByID | Get gene table from list of GeneIDs. |
| getIGraphFromPPI | Get Igraph representation of PPI |
| getInducedPPI4BrainRegion | Prepare induces network for compartment |
| getInducedPPI4Compartment | Prepare induces network for compartment |
| getLimitedPPI4BrainRegion | Prepare limited network for compartment |
| getLimitedPPI4Compartment | Prepare limited network for compartment |
| getMutations4DiseaseByEntres | Get mutational information for Gene and Disease |
| getMutations4DiseaseByIDs | Get mutational information for Gene and Disease |
| getMutations4DiseaseByName | Get mutational information for Gene and Disease |
| getMutDiseaseQuery | Prepare mutation access query |
| getPapers | Get synaptome papers overview |
| getPPIbyEntrez | Extract the PPIs for my list of genes defined by Entrez IDs |
| getPPIbyIDs | Extract the PPIs for my list of genes defined by GeneID |
| getPPIbyIDs4BrainRegion | Prepare induced or limited network for brain region |
| getPPIbyIDs4Compartment | Prepare induced or limited network for compartment |
| getPPIbyName | Extract the PPIs for my list of genes defined by Gene name |
| getPPIQuery | Prepare query for AllMutationAllPapers table |
| getTableFromPPI | Get table representation of the PPI. |
| graphFromSynaptomeByEntrez | Utility function to create network from 'synaptome.db' data |
| graphFromSynaptomeGeneTable | Utility function to create network from 'synaptome.db' data |
| synaptome.db | synaptome.db: programmatic access to the Synaptic proteome... |
