Files in nbenn/singleCellFeatures
Analyze single cell features stored in an openBIS instance
.gitignore
DESCRIPTION
NAMESPACE
R/Data.R
R/DataLocation.R
R/DataMeta.R
R/augmentAggregate.R
R/augmentBscore.R
R/augmentCordinateFeatures.R
R/augmentImageLocation.R
R/augmentMars.R
R/checkCompletenessFeature.R
R/checkCompletenessImage.R
R/checkCompletenessWell.R
R/checkConsistency.R
R/cleanData.R
R/convertToPlateLocation.R
R/convertToWellLocation.R
R/extractCells.R
R/extractFeatures.R
R/extractImages.R
R/extractWells.R
R/findDataLocations.R
R/getBarcode.R
R/getCacheFilenameData.R
R/getCacheFilenameMeta.R
R/getFeatureNames.R
R/getLocalPath.R
R/getNoImgPerWell.R
R/getOpenBisPath.R
R/getPathogen.R
R/getSingleCellData.R
R/getWellIndex.R
R/getWellName.R
R/glmBootstrap.R
R/makeFeatureCompatible.R
R/meltData.R
R/normalizeData.R
R/prepareDataforGlm.R
R/rebuildCache.R
R/saveToCache.R
R/utilDatabases.R
R/utilLocalData.R
R/utilPackage.R
R/utilPigz.R
R/visualizePlateData.R
R/zzz.R
all.sublime-project
data/featureDatabase.rda
data/plateDatabase.rda
data/wellDatabaseAdeno.rda
data/wellDatabaseBartonella.rda
data/wellDatabaseBrucella.rda
data/wellDatabaseListeria.rda
data/wellDatabaseMock.rda
data/wellDatabaseRhino.rda
data/wellDatabaseSalmonella.rda
data/wellDatabaseShigella.rda
data/wellDatabaseVaccinia.rda
man/ImageData.Rd
man/MatData.Rd
man/PlateAggregate.Rd
man/PlateData.Rd
man/PlateLocation.Rd
man/PlateMetadata.Rd
man/WellData.Rd
man/WellLocation.Rd
man/WellMetadata.Rd
man/analyzeSeparation.Rd
man/augmentAggregate.Rd
man/augmentBscore.Rd
man/augmentCordinateFeatures.Rd
man/augmentImageLocation.Rd
man/augmentMars.Rd
man/checkCompletenessFeature.Rd
man/checkCompletenessImage.Rd
man/checkCompletenessWell.Rd
man/checkConsistency.Rd
man/cleanData.Rd
man/compareModeltoTruth.Rd
man/configGet.Rd
man/configInit.Rd
man/configPathGet.Rd
man/configPathSet.Rd
man/configSet.Rd
man/convertToPlateLocation.Rd
man/convertToWellLocation.Rd
man/deleteAllMetadataCaches.Rd
man/deleteAllWellCaches.Rd
man/extractCells.Rd
man/extractFeatures.Rd
man/extractImages.Rd
man/extractWells.Rd
man/findPlates.Rd
man/findWells.Rd
man/getAllLocalPlates.Rd
man/getBarcode.Rd
man/getCacheFilenameData.Rd
man/getCacheFilenameMeta.Rd
man/getFeatureNames.Rd
man/getLocalPath.Rd
man/getNoImgPerWell.Rd
man/getNumCores.Rd
man/getOpenBisPath.Rd
man/getPathogen.Rd
man/getSingleCellData.Rd
man/getWellIndex1D.Rd
man/getWellIndex2D.Rd
man/getWellName.Rd
man/glmBootstrapStability.Rd
man/makeFeatureCompatible.Rd
man/makeRankFull.Rd
man/meltData.Rd
man/moveFeatures.Rd
man/normalizeData.Rd
man/normalizeMoltenData.Rd
man/plateBoxplot.Rd
man/plateHeatmap.Rd
man/prepareDataforGlm.Rd
man/processSingleCellDataPlate.Rd
man/readRDSMC.Rd
man/rebuildAllMatDataCaches.Rd
man/rebuildCache.Rd
man/reloadSingleCellFeatures.Rd
man/saveRDSMC.Rd
man/saveToCache.Rd
man/size.Rd
man/updateDatabaseFeatures.Rd
man/updateDatabasePlate.Rd
man/updateDatabaseWells.Rd
man/wellDatabaseCoverage.Rd
readme.md
vignettes/1-1_location_bruc-du.Rmd
vignettes/1-1_location_bruc-du.pdf
vignettes/1-2_ellipse_bruc-salm.Rmd
vignettes/1-2_ellipse_bruc-salm.pdf
vignettes/1-3_augmentation-features.Rmd
vignettes/1-3_augmentation-features.pdf
vignettes/2-1_glm-routines.Rmd
vignettes/2-1_glm-routines.pdf
vignettes/2-2_perfect-sep1-glm.Rmd
vignettes/2-2_perfect-sep1-glm.pdf
vignettes/2-3_perfect-sep2_brucella.Rmd
vignettes/2-5_stability-glmnet.Rmd
vignettes/2-6_stability_aggreggate.Rmd
vignettes/3-1-normalization-glm.Rmd
vignettes/3-2_normalized-stability.Rmd
vignettes/3-3_z-scored-stability.Rmd
