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Verbosity for Log Messaging", "topics": [ "getArchRVerbose" ] }, { "page": "getArrowFiles", "title": "Get ArrowFiles from an ArchRProject", "topics": [ "getArrowFiles" ] }, { "page": "getAvailableMatrices", "title": "Get a list available matrices in the ArrowFiles storted in an ArchRProject", "topics": [ "getAvailableMatrices" ] }, { "page": "getBgdPeaks", "title": "Get Background Peaks from an ArchRProject", "topics": [ "getBgdPeaks" ] }, { "page": "getBlacklist", "title": "Get the blacklist from an ArchRProject", "topics": [ "getBlacklist" ] }, { "page": "getCellColData", "title": "Get cellColData from an ArchRProject", "topics": [ "getCellColData" ] }, { "page": "getCellNames", "title": "Get cellNames from an ArchRProject", "topics": [ "getCellNames" ] }, { "page": "getChromLengths", "title": "Get chromLengths from ArchRProject", "topics": [ "getChromLengths" ] }, { "page": "getChromSizes", "title": "Get chromSizes from ArchRProject", "topics": [ "getChromSizes" ] }, { "page": "getCoAccessibility", "title": "Get the peak co-accessibility from an ArchRProject", "topics": [ "getCoAccessibility" ] }, { "page": "getEmbedding", "title": "Get embedding information stored in an ArchRProject", "topics": [ "getEmbedding" ] }, { "page": "getExons", "title": "Get the exons from an ArchRProject", "topics": [ "getExons" ] }, { "page": "getFeatures", "title": "Get the features that could be selected from a given data matrix within an ArchRProject", "topics": [ "getFeatures" ] }, { "page": "getFootprints", "title": "Calculate footprints from an ArchRProject", "topics": [ "getFootprints" ] }, { "page": "getFragmentsFromArrow", "title": "Get the fragments from an ArrowFile", "topics": [ "getFragmentsFromArrow" ] }, { "page": "getFragmentsFromProject", "title": "Get the fragments from an ArchRProject", "topics": [ "getFragmentsFromProject" ] }, { "page": "getGeneAnnotation", "title": "Get geneAnnotation from an ArchRProject", "topics": [ "getGeneAnnotation" ] }, { "page": "getGenes", "title": "Get the genes from an ArchRProject", "topics": [ "getGenes" ] }, { "page": "getGenome", "title": "Get the genome used by an ArchRProject", "topics": [ "getGenome" ] }, { "page": "getGenomeAnnotation", "title": "Get the genomeAnnotation from an ArchRProject", "topics": [ "getGenomeAnnotation" ] }, { "page": "getGroupBW", "title": "Export Group BigWigs", "topics": [ "getGroupBW" ] }, { "page": "getGroupFragments", "title": "Export Group Fragment Files", "topics": [ "getGroupFragments" ] }, { "page": "getGroupSE", "title": "Export Group Summarized Experiment", "topics": [ "getGroupSE" ] }, { "page": "getGroupSummary", "title": "Get summary for Groups in ArchRProject", "topics": [ "getGroupSummary" ] }, { "page": "getImputeWeights", "title": "Get Imputation Weights from ArchRProject", "topics": [ "getImputeWeights" ] }, { "page": "getInputFiles", "title": "Get Input Files from paths to create arrows", "topics": [ "getInputFiles" ] }, { "page": "getMarkerFeatures", "title": "Identify Marker Features for each cell grouping", "topics": [ "getMarkerFeatures" ] }, { "page": "getMarkers", "title": "Get Marker Features from a marker summarized experiment", "topics": [ "getMarkers" ] }, { "page": "getMatches", "title": "Get peak annotation matches from an ArchRProject", "topics": [ "getMatches" ] }, { "page": "getMatrixFromArrow", "title": "Get a data matrix stored in an ArrowFile", "topics": [ "getMatrixFromArrow" ] }, { "page": "getMatrixFromProject", "title": "Get a data matrix stored in an ArchRProject", "topics": [ "getMatrixFromProject" ] }, { "page": "getMonocleTrajectories", "title": "Get a Monocle CDS of Trajectories that can be added to an ArchRProject", "topics": [ "getMonocleTrajectories" ] }, { "page": "getOutputDirectory", "title": "Get outputDirectory from an ArchRProject", "topics": [ "getOutputDirectory" ] }, { "page": "getPBGroupSE", "title": "Export PseudoBulk Group Summarized Experiment", "topics": [ "getPBGroupSE" ] }, { "page": 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seqnames that could be selected from a given data matrix within an ArchRProject", "topics": [ "getSeqnames" ] }, { "page": "getTestArrow", "title": "Get PBMC Small Test Arrow file", "topics": [ "getTestArrow" ] }, { "page": "getTestFragments", "title": "Get PBMC Small Test Fragments", "topics": [ "getTestFragments" ] }, { "page": "getTestProject", "title": "Get PBMC Small Test Project", "topics": [ "getTestProject" ] }, { "page": "getTrajectory", "title": "Get Supervised Trajectory from an ArchR Project", "topics": [ "getTrajectory" ] }, { "page": "getTSS", "title": "Get the transcription start sites of all genes in an ArchRProject", "topics": [ "getTSS" ] }, { "page": "getTutorialData", "title": "Get Relevant Data For ArchR Tutorials", "topics": [ "getTutorialData" ] }, { "page": "getValidBarcodes", "title": "Get Valid Barcodes from 10x Cell Ranger output to pre-filter barcodes", "topics": [ "getValidBarcodes" ] }, { "page": "getVarDeviations", "title": "Get Variable Deviations across 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