analyzeSeparation | Find a hyperplane separating the sample points |
augmentAggregate | Augment PlateData with Aggregates |
augmentBscore | Augment PlateData with B-scores |
augmentCordinateFeatures | Augment all features involving locations |
augmentImageLocation | Augment the image location within a well |
augmentMars | Augment PlateData with MARS residuals |
checkCompletenessFeature | Check completeness of data |
checkCompletenessImage | Check if the set of images is complete |
checkCompletenessWell | Check if the set of wells is complete |
checkConsistency | Check consistency of Data object |
cleanData | Remove some bad image data |
compareModeltoTruth | Compare result of binary classification to truth |
configGet | Loads the config object |
configInit | Creates a config file template |
configPathGet | Get the config file path |
configPathSet | Set the config file path |
configSet | Overwrites the config file |
convertToPlateLocation | Covert compatible objects to PlateLocation |
convertToWellLocation | Covert compatible objects to WellLocation |
deleteAllMetadataCaches | Remove all metadata caches |
deleteAllWellCaches | Remove all local well caches |
extractCells | Extract cells from Data objects |
extractFeatures | Extract features from Data objects |
extractImages | Extract data for images from Data objects |
extractWells | Extract WellData objects form a PlateData object |
findPlates | Find PlateLocations |
findWells | Find WellLocations |
getAllLocalPlates | Get all local plates |
getBarcode | Get the barcode of a PlateLocation/WellLocation object |
getCacheFilenameData | Get path/filename of a PlateLocation/WellLocation object... |
getCacheFilenameMeta | Get the path/filename of the metadata chache for a... |
getFeatureNames | List feature names of a Data object |
getLocalPath | Get the local path of a PlateLocation/WellLocation object |
getNoImgPerWell | Get the number of images per Well |
getNumCores | Get the number of available cores |
getOpenBisPath | Get the path of a PlateLocation/WellLocation object on... |
getPathogen | Get the pathogen name of a PlateLocation/WellLocation object |
getSingleCellData | Read all single cell features for wells/plates |
getWellIndex1D | Linearize the index of a well on a 16x24 well plate |
getWellIndex2D | Get the 2D index of a well on a 16x24 well plate |
getWellName | Get the well name of a WellLocation object |
glmBootstrapStability | Analyze stability of top n coefficients |
ImageData | Constructor for ImageData objects |
makeFeatureCompatible | Enforce equal feature sets |
makeRankFull | Enforce full rank design matrix |
MatData | Constructor for MatData objects |
meltData | Combine all data in a given Data object |
moveFeatures | Move feature(s) to different group |
normalizeData | Normalize Datasets |
normalizeMoltenData | Normalize data |
PlateAggregate | Constructor for PlateAggregate objects |
plateBoxplot | Boxpolot of feature per well |
PlateData | Constructor for PlateData objects |
plateHeatmap | Plot a plate heatmap |
PlateLocation | Constructor for PlateLocation objects |
PlateMetadata | Constructor for PlateMetadata objects |
prepareDataforGlm | Prepare a dataset for GLM analysis |
processSingleCellDataPlate | Read all single cell features for wells/a plate |
readRDSMC | A wrapper around readRDS for faster reading of compressed... |
rebuildAllMatDataCaches | Rebuild all local plates |
rebuildCache | Rebuild cache files for certain Data objects |
reloadSingleCellFeatures | Reload the singleCellFeatures package |
saveRDSMC | A wrapper around saveRDS to enable multicore compression |
saveToCache | Build cache files for certain Data objects |
size | Get amount of storage used by an object |
updateDatabaseFeatures | Update the featureDatabase object |
updateDatabasePlate | Generate the plateDatabase object |
updateDatabaseWells | Generate the wellDatabasePathogen objects |
WellData | Constructor for WellData objects |
wellDatabaseCoverage | Assess the coverage provided by available metadata |
WellLocation | Constructor for WellLocation objects |
WellMetadata | Constructor for WellMetadata objects |
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