addArchRAnnotations()
|
Add ArchR annotations to an ArchRProject |
addArchRChrPrefix()
|
Add a globally-applied requirement for chromosome prefix |
addArchRDebugging()
|
Set ArchR Debugging |
addArchRGenome()
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Add a globally defined genome to all ArchR functions. |
addArchRLogging()
|
Set ArchR Logging |
addArchRThreads()
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Add a globally-applied number of threads to use for parallel computing. |
addArchRVerbose()
|
Set ArchR Verbosity for Log Messaging |
addBgdPeaks()
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Add Background Peaks to an ArchRProject |
addCellColData()
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Add information to cellColData in an ArchRProject |
addClusters()
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Add cluster information to an ArchRProject |
addCoAccessibility()
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Add Peak Co-Accessibility to an ArchRProject |
addCombinedDims()
|
Combine two or more modalities dimensionality reductions. |
addDemuxletResults()
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Add Demuxlet Results to ArchR Project |
addDeviationsMatrix()
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Add a matrix of deviations for a given peakAnnotation to Arrow Files in ArchRProject |
addDoubletScores()
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Add Doublet Scores to a collection of ArrowFiles or an ArchRProject |
addFeatureCounts()
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This function will add total counts of scATAC cells in provided features into ArchRProject. |
addFeatureMatrix()
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Add a feature matrix to an ArchRProject or a set of ArrowFiles |
addGeneExpressionMatrix()
|
Add Gene Expression Matrix to ArrowFiles or an ArchRProject |
addGeneIntegrationMatrix()
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Add a GeneIntegrationMatrix to ArrowFiles or an ArchRProject |
addGeneScoreMatrix()
|
Add GeneScoreMatrix to ArrowFiles or an ArchRProject |
addGroupCoverages()
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Add Group Coverages to an ArchRProject object |
addHarmony()
|
Add Harmony Batch Corrected Reduced Dims to an ArchRProject |
addImputeWeights()
|
Add Imputation Weights to an ArchRProject |
addIterativeLSI()
|
Add an Iterative LSI-based dimensionality reduction to an ArchRProject |
addModuleScore()
|
Add Module Scores to an ArchRProject |
addMonocleTrajectory()
|
Add a Monocle Trajectory to an ArchR Project #NEW |
addMotifAnnotations()
|
Add motif annotations to an ArchRProject |
addPeak2GeneLinks()
|
Add Peak2GeneLinks to an ArchRProject |
addPeakAnnotations()
|
Add peak annotations to an ArchRProject |
addPeakMatrix()
|
Add a Peak Matrix to the ArrowFiles of an ArchRProject |
addPeakSet()
|
Add a peak set to an ArchRProject |
addProjectSummary()
|
Add projectSummary to an ArchRProject |
addReproduciblePeakSet()
|
Add a Reproducible Peak Set to an ArchRProject |
addSampleColData()
|
Add information to sampleColData in an ArchRProject |
addSlingShotTrajectories()
|
Add a Slingshot Trajectories to an ArchR Project #NEW |
addTSNE()
|
Add a TSNE embedding of a reduced dimensions object to an ArchRProject |
addTileMatrix()
|
Add TileMatrix to ArrowFiles or an ArchRProject |
addTrajectory()
|
Add a Supervised Trajectory to an ArchR Project |
addUMAP()
|
Add a UMAP embedding of a reduced dimensions object to an ArchRProject |
getArchRChrPrefix()
|
Get a globally-applied requirement for chromosome prefix |
getArchRDebugging()
|
Get ArchR Debugging |
getArchRGenome()
|
Get the globally defined genome, the geneAnnotation, or genomeAnnotation objects associated with the globally defined genome. |
getArchRLogging()
|
Get ArchR Logging |
getArchRThreads()
|
Get globally-applied number of threads to use for parallel computing. |
getArchRVerbose()
|
Set ArchR Verbosity for Log Messaging |
getArrowFiles()
|
Get ArrowFiles from an ArchRProject |
getAvailableMatrices()
|
Get a list available matrices in the ArrowFiles storted in an ArchRProject |
getBgdPeaks()
|
Get Background Peaks from an ArchRProject |
getBlacklist()
|
Get the blacklist from an ArchRProject |
getCellColData()
|
Get cellColData from an ArchRProject |
getCellNames()
|
Get cellNames from an ArchRProject |
getChromLengths()
|
Get chromLengths from ArchRProject |
getChromSizes()
|
Get chromSizes from ArchRProject |
getCoAccessibility()
|
Get the peak co-accessibility from an ArchRProject |
getEmbedding()
|
Get embedding information stored in an ArchRProject |
getExons()
|
Get the exons from an ArchRProject |
getFeatures()
|
Get the features that could be selected from a given data matrix within an ArchRProject |
getFootprints()
|
Calculate footprints from an ArchRProject |
getFragmentsFromArrow()
|
Get the fragments from an ArrowFile |
getFragmentsFromProject()
|
Get the fragments from an ArchRProject |
getGeneAnnotation()
|
Get geneAnnotation from an ArchRProject |
getGenes()
|
Get the genes from an ArchRProject |
getGenome()
|
Get the genome used by an ArchRProject |
getGenomeAnnotation()
|
Get the genomeAnnotation from an ArchRProject |
getGroupBW()
|
Export Group BigWigs |
getGroupSE()
|
Export Group Summarized Experiment |
getGroupSummary()
|
Get summary for Groups in ArchRProject |
getImputeWeights()
|
Get Imputation Weights from ArchRProject |
getInputFiles()
|
Get Input Files from paths to create arrows |
getMarkerFeatures()
|
Identify Marker Features for each cell grouping |
getMarkers()
|
Get Marker Features from a marker summarized experiment |
getMatches()
|
Get peak annotation matches from an ArchRProject |
getMatrixFromArrow()
|
Get a data matrix stored in an ArrowFile |
getMatrixFromProject()
|
Get a data matrix stored in an ArchRProject |
getMonocleTrajectories()
|
Get a Monocle CDS of Trajectories that can be added to an ArchRProject #NEW |
getOutputDirectory()
|
Get outputDirectory from an ArchRProject |
getPeak2GeneLinks()
|
Get the peak-to-gene links from an ArchRProject |
getPeakAnnotation()
|
Get peakAnnotation from an ArchRProject |
getPeakSet()
|
Get the peak set from an ArchRProject |
getPositions()
|
Get peak annotation positions from an ArchRProject |
getProjectSummary()
|
Get projectSummary from an ArchRProject |
getReducedDims()
|
Get dimensionality reduction information stored in an ArchRProject |
getSampleColData()
|
Get sampleColData from an ArchRProject |
getSampleNames()
|
Get the sample names from an ArchRProject |
getSeqnames()
|
Get the seqnames that could be selected from a given data matrix within an ArchRProject |
getTSS()
|
Get the transcription start sites of all genes in an ArchRProject |
getTestFragments()
|
Get PBMC Small Test Fragments |
getTestProject()
|
Get PBMC Small Test Project |
getTrajectory()
|
Get Supervised Trajectory from an ArchR Project |
getTutorialData()
|
Get Relevant Data For ArchR Tutorials |
getValidBarcodes()
|
Get Valid Barcodes from 10x Cell Ranger output to pre-filter barcodes |
getVarDeviations()
|
Get Variable Deviations across cells in ArchRProject. |
ArchRBrowser()
|
Launch ArchR Genome Browser |
ArchRPalettes
|
List of color palettes that can be used in plots |
ggAlignPlots()
|
Align ggplot plots vertically or horizontally |
ggGroup()
|
A ggplot-based ridge/violin plot wrapper function |
ggHex()
|
A ggplot-based Hexplot wrapper function summary of points in a standardized manner |
ggOneToOne()
|
A ggplot-based one-to-one dot plot wrapper function |
ggPoint()
|
A ggplot-based dot plot wrapper function |
paletteContinuous()
|
Continuous Color Palette |
paletteDiscrete()
|
Optimized discrete color palette generation |
plotBrowserTrack()
|
Plot an ArchR Region Track |
plotEmbedding()
|
Visualize an Embedding from ArchR Project |
plotEnrichHeatmap()
|
Plot a Heatmap of Peak Annotation Hypergeometric Enrichment in Marker Peaks. |
plotFootprints()
|
Plot Footprints |
plotFragmentSizes()
|
Plot the fragment size distribution for each sample |
plotGroups()
|
Visualize Groups from ArchR Project |
plotMarkerHeatmap()
|
Plot a Heatmap of Identified Marker Features |
plotMarkers()
|
Plot Differential Markers |
plotPDF()
|
Plot PDF in outputDirectory of an ArchRProject |
plotPeak2GeneHeatmap()
|
Plot Peak2Gene Heatmap from an ArchRProject |
plotTSSEnrichment()
|
Plot a TSS Enrichment Plot for Each Sample |
plotTrajectory()
|
Visualize a Trajectory from ArchR Project |
plotTrajectoryHeatmap()
|
Plot a Heatmap of Features across a Trajectory |
theme_ArchR()
|
ggplot2 default theme for ArchR |