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 |
.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 |
.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 |
.importFM | 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 |
.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 |
.rowScale | Source code |
.rowZscores | Source code |
.safeSaveRDS | Source code |
.safeSubset | Source code |
.saveUWOT | Source code |
.simulateProjectDoublets | Source code |
.startLogging | Source code |
.summarizeJASPARMotifs | 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 |
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 |
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 |
determineOverlapCpp | 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 |
getArchRChrPrefix | Man page Source code |
getArchRDebugging | Man page Source code |
getArchRGenome | 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 |
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 |
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 |
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 |
subsetArchRProject | Man page |
subsetCells | Man page Source code |
tabulate2dCpp | Source code |
theme_ArchR | Man page |
validBSgenome | Man page Source code |
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