Man pages for nbenn/singleCellFeatures
Analyze single cell features stored in an openBIS instance

analyzeSeparationFind a hyperplane separating the sample points
augmentAggregateAugment PlateData with Aggregates
augmentBscoreAugment PlateData with B-scores
augmentCordinateFeaturesAugment all features involving locations
augmentImageLocationAugment the image location within a well
augmentMarsAugment PlateData with MARS residuals
checkCompletenessFeatureCheck completeness of data
checkCompletenessImageCheck if the set of images is complete
checkCompletenessWellCheck if the set of wells is complete
checkConsistencyCheck consistency of Data object
cleanDataRemove some bad image data
compareModeltoTruthCompare result of binary classification to truth
configGetLoads the config object
configInitCreates a config file template
configPathGetGet the config file path
configPathSetSet the config file path
configSetOverwrites the config file
convertToPlateLocationCovert compatible objects to PlateLocation
convertToWellLocationCovert compatible objects to WellLocation
deleteAllMetadataCachesRemove all metadata caches
deleteAllWellCachesRemove all local well caches
extractCellsExtract cells from Data objects
extractFeaturesExtract features from Data objects
extractImagesExtract data for images from Data objects
extractWellsExtract WellData objects form a PlateData object
findPlatesFind PlateLocations
findWellsFind WellLocations
getAllLocalPlatesGet all local plates
getBarcodeGet the barcode of a PlateLocation/WellLocation object
getCacheFilenameDataGet path/filename of a PlateLocation/WellLocation object...
getCacheFilenameMetaGet the path/filename of the metadata chache for a...
getFeatureNamesList feature names of a Data object
getLocalPathGet the local path of a PlateLocation/WellLocation object
getNoImgPerWellGet the number of images per Well
getNumCoresGet the number of available cores
getOpenBisPathGet the path of a PlateLocation/WellLocation object on...
getPathogenGet the pathogen name of a PlateLocation/WellLocation object
getSingleCellDataRead all single cell features for wells/plates
getWellIndex1DLinearize the index of a well on a 16x24 well plate
getWellIndex2DGet the 2D index of a well on a 16x24 well plate
getWellNameGet the well name of a WellLocation object
glmBootstrapStabilityAnalyze stability of top n coefficients
ImageDataConstructor for ImageData objects
makeFeatureCompatibleEnforce equal feature sets
makeRankFullEnforce full rank design matrix
MatDataConstructor for MatData objects
meltDataCombine all data in a given Data object
moveFeaturesMove feature(s) to different group
normalizeDataNormalize Datasets
normalizeMoltenDataNormalize data
PlateAggregateConstructor for PlateAggregate objects
plateBoxplotBoxpolot of feature per well
PlateDataConstructor for PlateData objects
plateHeatmapPlot a plate heatmap
PlateLocationConstructor for PlateLocation objects
PlateMetadataConstructor for PlateMetadata objects
prepareDataforGlmPrepare a dataset for GLM analysis
processSingleCellDataPlateRead all single cell features for wells/a plate
readRDSMCA wrapper around readRDS for faster reading of compressed...
rebuildAllMatDataCachesRebuild all local plates
rebuildCacheRebuild cache files for certain Data objects
reloadSingleCellFeaturesReload the singleCellFeatures package
saveRDSMCA wrapper around saveRDS to enable multicore compression
saveToCacheBuild cache files for certain Data objects
sizeGet amount of storage used by an object
updateDatabaseFeaturesUpdate the featureDatabase object
updateDatabasePlateGenerate the plateDatabase object
updateDatabaseWellsGenerate the wellDatabasePathogen objects
WellDataConstructor for WellData objects
wellDatabaseCoverageAssess the coverage provided by available metadata
WellLocationConstructor for WellLocation objects
WellMetadataConstructor for WellMetadata objects
nbenn/singleCellFeatures documentation built on May 23, 2019, 12:24 p.m.