Files in khodosevichlab/CellAnnotatoR

Automated marker-based cell type annotation

.Rbuildignore

.gitignore

CHANGELOG.md

CellAnnotatoR.Rproj

CellAnnotatoR.pdf

DESCRIPTION

NAMESPACE

R/RcppExports.R R/annotation.R R/confidence_estimation.R R/hierarchies.R R/marker_selection.R R/markup_processing.R R/plots.R R/utils.R README.md inst/extdata/bm_cb.md man/aggregateScoreChangePerGene.Rd man/arrangePlots.Rd man/assignCellsByScores.Rd man/classificationTreeToDf.Rd man/createClassificationTree.Rd man/deriveHierarchy.Rd man/diffuseGraph.Rd man/diffuseScorePerType.Rd man/extractCellTypeProbs.Rd man/extractMarkersFromSubtypes.Rd man/getAnnotationPerParent.Rd man/getCellTypeScoreInfo.Rd man/getClassificationData.Rd man/getMarkerScoreInfo.Rd man/getMarkerScoresPerCellType.Rd man/getTopNegativeGenes.Rd man/hierarchyToClassificationTree.Rd man/markerListToMarkup.Rd man/mergeAnnotationByLevels.Rd man/mergeAnnotationToLevel.Rd man/mergeScoreInfos.Rd man/mergeScores.Rd man/normalizeTCWithFeatures.Rd man/normalizeTfIdfWithFeatures.Rd man/parseMarkerFile.Rd man/plapply.Rd man/plotAssignmentScores.Rd man/plotGeneExpression.Rd man/plotMarkerListViolinMap.Rd man/plotOneUncertaintyPerClust.Rd man/plotSubtypeMarkers.Rd man/plotTypeMarkers.Rd man/plotUncertaintyPerCell.Rd man/plotUncertaintyPerClust.Rd man/prepareDeInfo.Rd man/scoreCellUncertaintyPerLevel.Rd man/scoreClusterUncertaintyPerLevel.Rd man/scorePerCellUncertainty.Rd man/selectMarkersPerType.Rd markers/mca_lung.md markers/pbmc.md

src/.gitignore

src/RcppExports.cpp

src/functions.cpp

tests/testthat.R tests/testthat/test_annotation.R tests/testthat/test_parser.R

vignettes/.gitignore

vignettes/conos_bm_cb.Rmd vignettes/conos_bm_cb.md

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vignettes/mca_marker_selection.Rmd vignettes/mca_marker_selection.md

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vignettes/mca_qc.Rmd vignettes/mca_qc.md

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vignettes/pagoda_bm.Rmd vignettes/pagoda_bm.md

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vignettes/seurat_pbmc3k.Rmd vignettes/seurat_pbmc3k.md

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khodosevichlab/CellAnnotatoR documentation built on June 29, 2022, 9:12 p.m.