Man pages for vitkl/MItools
Protein interaction data tools: retrieving data from IntAct and most other databases using PSICQUIC service
| browseMIontology | browse Molecular Interaction ontology |
| cleanMITAB | Process molecular interaction data in MITAB 2.5 or 2.7... |
| cleanMITAB25 | 'cleanMITAB' extracts and cleans a set of columns of MITAB2.5 |
| cleanMITAB27 | 'cleanMITAB' extracts and cleans a set of columns of MITAB2.7 |
| edgelist2degree | find the degree for each protein given cleaned molecular... |
| edgelist2degreeFreq | Find the degree distribution given edgelist (pair_id) and a... |
| extractInteractors | Subset MITAB to retrieve interactors, the number of... |
| fullInteractome | Retrieve interactome (proteins only or not) of a given... |
| humanViralDegree | Compare viral and human protein degree distribution, filter... |
| interactorFeatureTypes | discover types of interactor features in MITAB 2.7 |
| interSpeciesInteractome | Retrieve interspecies interactions (proteins only or not) for... |
| lastIntActRelease | last IntAct (all IMEx databases) release |
| loadAllIDProteins | load the list of all protein ID in UniProtKB |
| loadBioplex | load Bioplex data |
| loadHumanViralPPI | load human-human, human-viral and viral-viral PPI data from... |
| loadIntActFTP | load all data from IntAct ftp |
| loadMIontology | load Molecular Interaction ontology |
| loadTaxIDAllLower | load all lower taxonomy ID (all descendants) |
| loadTaxIDProteins | load the list of all proteins for given taxonomy ID (any... |
| MITABregionFeature | Extract binding region feature from cleaned MITAB2.7 |
| queryPSICQUIC | Use PSICQUIC to query for molecular interactions (using MIQL,... |
| queryPSICQUICrlib | download PSICQUIC query search result (only IMEx databases)... |
| randomInteractome | Retrieve molecular interactions for the random set of... |
| readInteractome | read Interactome into data.table |
| removeInteractionNoFASTA | Remove interactions if one participant doesn't have FASTA... |
| removeInteractionObsoleteID | Remove interactions if one participant has obsolete Uniprot... |
| removeSelfLoops | Remove self loops (self-interactions) |
| reorderMITAB25 | 'reorderMITAB25' reorders interacting molecules in a pair... |
| reorderMITAB27 | 'reorderMITAB27' reorders interacting molecules in a pair... |
| subsetMITABbyID | Retrieve interactions for a list of interactors (given data... |
| subsetMITABbyMethod | Filter molecular interactions by interaction detection... |
| subsetMITABbyPMIDs | Filter molecular interactions by Pubmed ID |
