Man pages for girke-lab/bioassayR
Cross-target analysis of small molecule bioactivity
| activeAgainst | Show compounds active against a specified target |
| activeTargets | Show targets against which a small molecule is active |
| addBioassayIndex | Index a bioassayR database |
| addDataSource | Add a new data source to a bioassayR database |
| allCids | List compound cids in a 'BioassayDB', 'bioassay',... |
| allTargets | List distinct target(s) in a 'BioassayDB', 'bioassay',... |
| assaySetTargets | Return targets of assays in a 'bioassaySet' object |
| bioactivityFingerprint | Create an 'ChemmineR' 'FPset' object that contains... |
| bioassay-class | Class '"bioassay"' |
| BioAssayDB-class | Class '"BioassayDB"' |
| bioassaySet-class | Class '"bioassaySet"' |
| connectBioassayDB | Create a 'BioassayDB' object connected to the specified... |
| crossReactivityProbability | Compute the probability that compounds in a compound vs... |
| disconnectBioassayDB | Disconnect the database file from a 'BioassayDB' object |
| dropBioassay | Delete an assay from a bioassayR database |
| dropBioassayIndex | Remove index from a bioassayR database |
| getAssay | Retrieve a bioassay |
| getAssays | Retrieve multiple bioassays from a database |
| getBioassaySetByCids | Create 'bioassaySet' sparse matrix object with activity data... |
| inactiveTargets | Takes a single cid and returns a table of the proteins it has... |
| loadBioassay | Add an assay to the database |
| loadIdMapping | Load a target identifier mapping into a bioassayR database |
| newBioassayDB | Create a new bioassayR database |
| parsePubChemBioassay | Parse PubChem Bioassay Data |
| perTargetMatrix | Collapse a 'bioassaySet' object from multiple assays by... |
| queryBioassayDB | Perform a SQL query on a bioassayR database |
| samplebioassay | Sample activity data for use with bioassayR |
| scaleBioassaySet | Centers and standardizes the numeric activity scores for a... |
| screenedAtLeast | Return all compounds in the database screened at least... |
| selectiveAgainst | Identify small molecules with selective binding against a... |
| targetSelectivity | Returns the target selectivity for a specified list of... |
| translateTargetId | Translate a protein target identifier to another identifier... |
| trinarySimilarity | Computes the tanimoto similarity coefficient between the... |
