API for GreenleafLab/ArchR
Analyzing single-cell regulatory chromatin in R.
| Global functions | |
|---|---|
| $.ArchRProject | Man page |
| $<-.ArchRProject | Man page |
| %bcin% | Man page |
| %bcni% | Man page |
| %ni% | Man page |
| .ArchRHeatmap | Source code |
| .DollarNames.ArchRProject | Man page |
| .LSIPartialMatrix | Source code |
| .MarkersSC | Source code |
| .addDeviationsMatrix | Source code |
| .addDoubScores | Source code |
| .addFeatureMatrix | Source code |
| .addGeneExpressionMat | Source code |
| .addGeneScoreMat | Source code |
| .addKmerBiasToCoverage | Source code |
| .addMatToArrow | Source code |
| .addTileMat | Source code |
| .availableArrays | Source code |
| .binarySort | Source code |
| .bulkTracks | Source code |
| .checkJupyter | Source code |
| .checkShowLegend | Source code |
| .colBinarySums | Source code |
| .colorMapAnno | Source code |
| .colorMapForCH | Source code |
| .computeKNN | Source code |
| .computeROC | Source code |
| .createArrow | Source code |
| .createCoverages | Source code |
| .customDeviations | Source code |
| .downloadFiles | Source code |
| .endLogging | Source code |
| .expm1 | Source code |
| .fastFeatureCounts | Source code |
| .fastFragmentInfo | Source code |
| .fastTSSCounts | Source code |
| .fastTSSEnrichment | Source code |
| .getBlacklist | Source code |
| .getCoverageInsertionSites | Source code |
| .getCoverageMetadata | Source code |
| .getCoverageParams | Source code |
| .getCoverageRle | Source code |
| .getFragsFromArrow | Source code |
| .getMatrixValues | Source code |
| .getOrgDb | Source code |
| .getQuantiles | Source code |
| .getTxDb | Source code |
| .groupMeans | Source code |
| .groupRegionSumArrows | Source code |
| .identifyGroupsForPseudoBulk | Source code |
| .import10xToSE | Source code |
| .initializeMat | Source code |
| .isBam | Source code |
| .isColor | Source code |
| .isDiscrete | Source code |
| .isGRList | Source code |
| .isProtectedArray | Source code |
| .isTabix | Source code |
| .isWholenumber | Source code |
| .leastOverlapCells | Source code |
| .loadUWOT | Source code |
| .log2p1 | Source code |
| .logDiffTime | Source code |
| .logError | Source code |
| .logHeader | Source code |
| .logMessage | Source code |
| .logStop | Source code |
| .logThis | Source code |
| .mergeParams | Source code |
| .messageDiffTime | Source code |
| .normalizeCols | Source code |
| .onAttach | Source code |
| .quantileCut | Source code |
| .requirePackage | Source code |
| .rowBinarySums | Source code |
| .rowScale | Source code |
| .rowZscores | Source code |
| .safeSaveRDS | Source code |
| .safeSubset | Source code |
| .saveUWOT | Source code |
| .simulateProjectDoublets | Source code |
| .sortRSE | Source code |
| .sparesRowSds | Source code |
| .sparseColLog2p1Means | Source code |
| .sparseRowGeoDisp | Source code |
| .sparseRowGeoMeans | Source code |
| .sparseRowGeoVars | Source code |
| .sparseRowLog2p1Means | Source code |
| .sparseRowLog2p1Vars | Source code |
| .sparseRowScale | Source code |
| .sparseRowVars | Source code |
| .sparseRowVarsStd | Source code |
| .startLogging | Source code |
| .summarizeJASPARMotifs | Source code |
| .suppressSpecificWarnings | Man page Source code |
| .tabixToTmp | Source code |
| .validArchRProject | Source code |
| .validArrow | Source code |
| .validArrowFiles | Source code |
| .validGRanges | Source code |
| .validGeneAnnoByGenomeAnno | Source code |
| .validGeneAnnotation | Source code |
| .validGenomeAnnotation | Source code |
| .validInput | Source code |
| .validOrgDb | Source code |
| .validTxDb | Source code |
| .writeCoverageToBed | Source code |
| ArchRBrowser | Man page Source code |
| ArchRBrowserTrack | Source code |
| ArchRHeatmap | Man page Source code |
| ArchRPalettes | Man page |
| ArchRProject | Man page Source code |
| [.ArchRProject | Man page |
| addArchRAnnotations | Man page |
| addArchRChrPrefix | Man page Source code |
| addArchRDebugging | Man page Source code |
| addArchRGenome | Man page Source code |
| addArchRH5Level | Man page Source code |
| addArchRLocking | Man page Source code |
| addArchRLogging | Man page Source code |
| addArchRThreads | Man page Source code |
| addArchRVerbose | Man page Source code |
| addBgdPeaks | Man page |
| addCellColData | Man page |
| addClusters | Man page Source code |
| addCoAccessibility | Man page |
| addCombinedDims | Man page Source code |
| addDemuxletResults | Man page |
| addDeviationsMatrix | Man page Source code |
| addDoubletScores | Man page Source code |
| addFeatureCounts | Man page |
| addFeatureMatrix | Man page Source code |
| addGeneExpressionMatrix | Man page Source code |
| addGeneIntegrationMatrix | Man page Source code |
| addGeneScoreMatrix | Man page Source code |
| addGroupCoverages | Man page Source code |
| addHarmony | Man page Source code |
| addImputeWeights | Man page Source code |
| addIterativeLSI | Man page Source code |
| addModuleScore | Man page Source code |
| addMonocleTrajectory | Man page |
| addMotifAnnotations | Man page Source code |
| addPeak2GeneLinks | Man page |
| addPeakAnnotations | Man page Source code |
| addPeakMatrix | Man page Source code |
| addPeakSet | Man page |
| addProjectSummary | Man page |
| addReproduciblePeakSet | Man page Source code |
| addSampleColData | Man page Source code |
| addSlingShotTrajectories | Man page |
| addTSNE | Man page Source code |
| addTileMatrix | Man page Source code |
| addTrajectory | Man page Source code |
| addUMAP | Man page Source code |
| computeSparseRowVariances | Source code |
| confusionMatrix | Man page Source code |
| correlateMatrices | Man page Source code |
| correlateTrajectories | Man page |
| createArrowFiles | Man page Source code |
| createGeneAnnotation | Man page Source code |
| createGenomeAnnotation | Man page Source code |
| createLogFile | Man page Source code |
| customEnrichment | Man page |
| determineOverlapCpp | Source code |
| deviations_cpp | Source code |
| error | Source code |
| exportGroupSE | Source code |
| exportPeakMatrixForSTREAM | Man page |
| extendGR | Man page Source code |
| filterChrGR | Man page Source code |
| filterDoublets | Man page Source code |
| findMacs2 | Man page |
| find_non_zero_indices | Source code |
| getArchRChrPrefix | Man page Source code |
| getArchRDebugging | Man page Source code |
| getArchRGenome | Man page Source code |
| getArchRH5Level | Man page Source code |
| getArchRLogging | Man page Source code |
| getArchRThreads | Man page Source code |
| getArchRVerbose | Man page Source code |
| getArrowFiles | Man page Source code |
| getAvailableMatrices | Man page |
| getBgdPeaks | Man page |
| getBlacklist | Man page |
| getCellColData | Man page Source code |
| getCellNames | Man page Source code |
| getChromLengths | Man page |
| getChromSizes | Man page |
| getCoAccessibility | Man page |
| getEmbedding | Man page |
| getExons | Man page |
| getFeatures | Man page |
| getFootprints | Man page Source code |
| getFragmentsFromArrow | Man page Source code |
| getFragmentsFromProject | Man page Source code |
| getGeneAnnotation | Man page |
| getGenes | Man page |
| getGenome | Man page |
| getGenomeAnnotation | Man page |
| getGroupBW | Man page |
| getGroupFragments | Man page |
| getGroupSE | Man page Source code |
| getGroupSummary | Man page Source code |
| getImputeWeights | Man page Source code |
| getInputFiles | Man page Source code |
| getMarkerFeatures | Man page Source code |
| getMarkers | Man page |
| getMatches | Man page Source code |
| getMatrixFromArrow | Man page |
| getMatrixFromProject | Man page Source code |
| getMonocleTrajectories | Man page |
| getOutputDirectory | Man page Source code |
| getPBGroupSE | Man page |
| getPeak2GeneLinks | Man page |
| getPeakAnnotation | Man page Source code |
| getPeakSet | Man page |
| getPositions | Man page Source code |
| getProjectSummary | Man page |
| getReducedDims | Man page |
| getSampleColData | Man page Source code |
| getSampleNames | Man page Source code |
| getSeqnames | Man page |
| getTSS | Man page |
| getTestArrow | Man page Source code |
| getTestFragments | Man page Source code |
| getTestProject | Man page Source code |
| getTrajectory | Man page |
| getTutorialData | Man page Source code |
| getValidBarcodes | Man page Source code |
| getVarDeviations | Man page |
| ggAlignPlots | Man page |
| ggGroup | Man page |
| ggHex | Man page |
| ggOneToOne | Man page |
| ggPoint | Man page Source code |
| import10xFeatureMatrix | Man page Source code |
| imputeMatrix | Man page Source code |
| installExtraPackages | Man page Source code |
| kmerIDFrequencyCpp | Source code |
| kmerIdxCpp | Source code |
| kmerPositionFrequencyCpp | Source code |
| loadArchRProject | Man page |
| mapLabels | Man page Source code |
| markerFeatures | Source code |
| nCells | Man page Source code |
| nonOverlappingGR | Man page Source code |
| paletteContinuous | Man page Source code |
| paletteDiscrete | Man page Source code |
| peakAnnoEnrichment | Man page |
| plotBrowserTrack | Man page Source code |
| plotEmbedding | Man page Source code |
| plotEnrichHeatmap | Man page |
| plotFootprints | Man page |
| plotFragmentSizes | Man page |
| plotGroups | Man page Source code |
| plotMarkerHeatmap | Man page |
| plotMarkers | Man page |
| plotPDF | Man page Source code |
| plotPeak2GeneHeatmap | Man page |
| plotTSSEnrichment | Man page Source code |
| plotTrajectory | Man page |
| plotTrajectoryHeatmap | Man page |
| projectBulkATAC | Man page Source code |
| recoverArchRProject | Man page |
| reformatFragmentFiles | Man page Source code |
| rleSumsStranded | Source code |
| rleSumsStrandedChr | Source code |
| rowCorCpp | Source code |
| saveArchRProject | Man page |
| setArchRLocking | Man page Source code |
| subsetArchRProject | Man page |
| subsetCells | Man page Source code |
| tabulate2dCpp | Source code |
| theme_ArchR | Man page |
| validBSgenome | Man page Source code |
| warning | Source code |
