Files in GreenleafLab/ArchR
Analyzing single-cell regulatory chromatin in R.

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ArchR.Rproj

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NAMESPACE

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R/AllClasses.R R/AnnotationGenome.R R/AnnotationPeaks.R R/ArchRBrowser.R R/ArchRHeatmap.R R/ArrowRead.R R/ArrowUtils.R R/ArrowWrite.R R/BulkProjection.R R/Clustering.R R/ColorPalettes.R R/CreateArrow.R R/DoubletsScores.R R/Embedding.R R/FilterCells.R R/Footprinting.R R/GRangesUtils.R R/GgplotUtils.R R/GlobalDefaults.R R/GroupCoverages.R R/GroupExport.R R/Harmony.R R/HelperUtils.R R/HiddenUtils.R R/Imputation.R R/InputData.R R/IntegrativeAnalysis.R R/IterativeLSI.R R/LoggerUtils.R R/MarkerFeatures.R R/MatrixDeviations.R R/MatrixFeatures.R R/MatrixGeneExpression.R R/MatrixGeneScores.R R/MatrixTiles.R R/ModuleScore.R R/MultiModal.R R/ProjectMethods.R R/QualityControl.R R/RNAIntegration.R R/RcppExports.R R/ReproduciblePeakSet.R R/Trajectory.R R/ValidationUtils.R R/VisualizeData.R README.md

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data/.DS_Store

data/geneAnnoHg19.rda

data/geneAnnoHg19test.rda

data/geneAnnoHg38.rda

data/geneAnnoMm10.rda

data/geneAnnoMm9.rda

data/genomeAnnoHg19.rda

data/genomeAnnoHg19test.rda

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data/genomeAnnoMm10.rda

data/genomeAnnoMm9.rda

docs/.DS_Store

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man/.DS_Store

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man/.Rhistory

man/ArchRBrowser.Rd man/ArchRPalettes.Rd man/ArchRProject.Rd man/addArchRAnnotations.Rd man/addArchRChrPrefix.Rd man/addArchRDebugging.Rd man/addArchRGenome.Rd man/addArchRLogging.Rd man/addArchRThreads.Rd man/addArchRVerbose.Rd man/addBgdPeaks.Rd man/addCellColData.Rd man/addClusters.Rd man/addCoAccessibility.Rd man/addCombinedDims.Rd man/addDemuxletResults.Rd man/addDeviationsMatrix.Rd man/addDoubletScores.Rd man/addFeatureCounts.Rd man/addFeatureMatrix.Rd man/addGeneExpressionMatrix.Rd man/addGeneIntegrationMatrix.Rd man/addGeneScoreMatrix.Rd man/addGroupCoverages.Rd man/addHarmony.Rd man/addImputeWeights.Rd man/addIterativeLSI.Rd man/addModuleScore.Rd man/addMonocleTrajectory.Rd man/addMotifAnnotations.Rd man/addPeak2GeneLinks.Rd man/addPeakAnnotations.Rd man/addPeakMatrix.Rd man/addPeakSet.Rd man/addProjectSummary.Rd man/addReproduciblePeakSet.Rd man/addSampleColData.Rd man/addSlingShotTrajectories.Rd man/addTSNE.Rd man/addTileMatrix.Rd man/addTrajectory.Rd man/addUMAP.Rd man/cash-.ArchRProject.Rd man/cash-set-.ArchRProject.Rd man/confusionMatrix.Rd man/correlateMatrices.Rd man/correlateTrajectories.Rd man/createArrowFiles.Rd man/createGeneAnnotation.Rd man/createGenomeAnnotation.Rd man/createLogFile.Rd man/dot-DollarNames.ArchRProject.Rd man/exportPeakMatrixForSTREAM.Rd man/extendGR.Rd

man/figures/ArchR_Workflow.png

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man/filterChrGR.Rd man/filterDoublets.Rd man/findMacs2.Rd man/getArchRChrPrefix.Rd man/getArchRDebugging.Rd man/getArchRGenome.Rd man/getArchRLogging.Rd man/getArchRThreads.Rd man/getArchRVerbose.Rd man/getArrowFiles.Rd man/getAvailableMatrices.Rd man/getBgdPeaks.Rd man/getBlacklist.Rd man/getCellColData.Rd man/getCellNames.Rd man/getChromLengths.Rd man/getChromSizes.Rd man/getCoAccessibility.Rd man/getEmbedding.Rd man/getExons.Rd man/getFeatures.Rd man/getFootprints.Rd man/getFragmentsFromArrow.Rd man/getFragmentsFromProject.Rd man/getGeneAnnotation.Rd man/getGenes.Rd man/getGenome.Rd man/getGenomeAnnotation.Rd man/getGroupBW.Rd man/getGroupSE.Rd man/getGroupSummary.Rd man/getImputeWeights.Rd man/getInputFiles.Rd man/getMarkerFeatures.Rd man/getMarkers.Rd man/getMatches.Rd man/getMatrixFromArrow.Rd man/getMatrixFromProject.Rd man/getMonocleTrajectories.Rd man/getOutputDirectory.Rd man/getPeak2GeneLinks.Rd man/getPeakAnnotation.Rd man/getPeakSet.Rd man/getPositions.Rd man/getProjectSummary.Rd man/getReducedDims.Rd man/getSampleColData.Rd man/getSampleNames.Rd man/getSeqnames.Rd man/getTSS.Rd man/getTestFragments.Rd man/getTestProject.Rd man/getTrajectory.Rd man/getTutorialData.Rd man/getValidBarcodes.Rd man/getVarDeviations.Rd man/ggAlignPlots.Rd man/ggGroup.Rd man/ggHex.Rd man/ggOneToOne.Rd man/ggPoint.Rd man/grapes-bcin-grapes.Rd man/grapes-bcni-grapes.Rd man/grapes-ni-grapes.Rd man/import10xFeatureMatrix.Rd man/imputeMatrix.Rd man/installExtraPackages.Rd man/loadArchRProject.Rd man/mapLabels.Rd man/nCells.Rd man/nonOverlappingGR.Rd man/paletteContinuous.Rd man/paletteDiscrete.Rd man/peakAnnoEnrichment.Rd man/plotBrowserTrack.Rd man/plotEmbedding.Rd man/plotEnrichHeatmap.Rd man/plotFootprints.Rd man/plotFragmentSizes.Rd man/plotGroups.Rd man/plotMarkerHeatmap.Rd man/plotMarkers.Rd man/plotPDF.Rd man/plotPeak2GeneHeatmap.Rd man/plotTSSEnrichment.Rd man/plotTrajectory.Rd man/plotTrajectoryHeatmap.Rd man/projectBulkATAC.Rd man/recoverArchRProject.Rd man/reformatFragmentFiles.Rd man/saveArchRProject.Rd man/sub-.ArchRProject.Rd man/subsetArchRProject.Rd man/subsetCells.Rd man/theme_ArchR.Rd man/validBSgenome.Rd

src/.DS_Store

src/.gitignore

src/Correlation.cpp

src/Footprinting_utils.cpp

src/General_Utils.cpp

src/KNN_Utils.cpp

src/Kmer_Bias.cpp

src/RcppExports.cpp

GreenleafLab/ArchR documentation built on Feb. 28, 2024, 4:17 p.m.

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GreenleafLab/ArchR
Analyzing single-cell regulatory chromatin in R.

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Analyzing single-cell regulatory chromatin in R.

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GreenleafLab/ArchR Analyzing single-cell regulatory chromatin in R.

Files in GreenleafLab/ArchR Analyzing single-cell regulatory chromatin in R.

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GreenleafLab/ArchR
Analyzing single-cell regulatory chromatin in R.

Files in GreenleafLab/ArchR
Analyzing single-cell regulatory chromatin in R.