Analyzing single-cell regulatory chromatin in R.
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Documentation for package ‘ArchR’ version 1.0.3
Help Pages
A C E F G I L M N P R S T V misc
-- A --
| addArchRAnnotations | Add ArchR annotations to an ArchRProject |
| addArchRChrPrefix | Add a globally-applied requirement for chromosome prefix |
| addArchRDebugging | Set ArchR Debugging |
| addArchRGenome | Add a globally defined genome to all ArchR functions. |
| addArchRH5Level | Add a globally-applied compression level for h5 files |
| addArchRLocking | Add a globally-applied H5 file locking setup |
| addArchRLogging | Set ArchR Logging |
| addArchRThreads | Add a globally-applied number of threads to use for parallel computing. |
| addArchRVerbose | Set ArchR Verbosity for Log Messaging |
| addBgdPeaks | Add Background Peaks to an ArchRProject |
| addCellColData | Add information to cellColData in an ArchRProject |
| addClusters | Add cluster information to an ArchRProject |
| addCoAccessibility | Add Peak Co-Accessibility to an ArchRProject |
| addCombinedDims | Combine two or more modalities dimensionality reductions. |
| addDemuxletResults | Add Demuxlet Results to ArchR Project |
| addDeviationsMatrix | Add a matrix of deviations for a given peakAnnotation to Arrow Files in ArchRProject |
| addDoubletScores | Add Doublet Scores to a collection of ArrowFiles or an ArchRProject |
| addFeatureCounts | This function will add total counts of scATAC cells in provided features into ArchRProject. |
| addFeatureMatrix | Add a feature matrix to an ArchRProject or a set of ArrowFiles |
| addGeneExpressionMatrix | Add Gene Expression Matrix to ArrowFiles or an ArchRProject |
| addGeneIntegrationMatrix | Add a GeneIntegrationMatrix to ArrowFiles or an ArchRProject |
| addGeneScoreMatrix | Add GeneScoreMatrix to ArrowFiles or an ArchRProject |
| addGroupCoverages | 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 |
| 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 |
| addTileMatrix | Add TileMatrix to ArrowFiles or an ArchRProject |
| addTrajectory | Add a Supervised Trajectory to an ArchR Project |
| addTSNE | Add a TSNE embedding of a reduced dimensions object to an ArchRProject |
| addUMAP | Add a UMAP embedding of a reduced dimensions object to an ArchRProject |
| ArchRBrowser | Launch ArchR Genome Browser |
| ArchRHeatmap | Plot Nice Lookng Heatmap Using Complex Heatmap |
| ArchRPalettes | List of color palettes that can be used in plots |
| ArchRProject | Create ArchRProject from ArrowFiles |
-- C --
| confusionMatrix | Create a Confusion Matrix based on two value vectors |
| correlateMatrices | Correlate Matrices within an ArchRProject |
| correlateTrajectories | Correlate Trajectories |
| createArrowFiles | Create Arrow Files |
| createGeneAnnotation | Create a gene annotation object for ArchR |
| createGenomeAnnotation | Create a genome annotation object for ArchR |
| createLogFile | Create a Log File for ArchR |
| customEnrichment | Hypergeometric Enrichment in input peak ranges. |
-- E --
| exportPeakMatrixForSTREAM | Get a PeakMatrix stored in an ArchRProject and write out for STREAM |
| extendGR | Extend regions from a Genomic Ranges object |
-- F --
| filterChrGR | Filters unwanted seqlevels from a Genomic Ranges object or similar object |
| filterDoublets | Filter Doublets From an ArchRProject |
| findMacs2 | Find the installed location of the MACS2 executable |
-- G --
| 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. |
| getArchRH5Level | Get globally-applied compression level for h5 files |
| 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 |
| getGroupFragments | Export Group Fragment Files |
| 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 |
| getOutputDirectory | Get outputDirectory from an ArchRProject |
| getPBGroupSE | Export PseudoBulk Group Summarized Experiment |
| 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 |
| getTestArrow | Get PBMC Small Test Arrow file |
| getTestFragments | Get PBMC Small Test Fragments |
| getTestProject | Get PBMC Small Test Project |
| getTrajectory | Get Supervised Trajectory from an ArchR Project |
| getTSS | Get the transcription start sites of all genes in an ArchRProject |
| 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. |
| 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 |
-- I --
| import10xFeatureMatrix | Import Feature Matrix from 10x Feature HDF5 file. |
| imputeMatrix | Impute a matrix with impute weights |
| installExtraPackages | Install extra packages used in ArchR that are not installed by default |
-- L --
| loadArchRProject | Load Previous ArchRProject into R |
-- M --
| mapLabels | Re-map a character vector of labels from an old set of labels to a new set of labels |
-- N --
| nCells | Get the number of cells from an ArchRProject/ArrowFile |
| nonOverlappingGR | Retreive a non-overlapping set of regions from a Genomic Ranges object |
-- P --
| paletteContinuous | Continuous Color Palette |
| paletteDiscrete | Optimized discrete color palette generation |
| peakAnnoEnrichment | Peak Annotation Hypergeometric Enrichment in Marker Peaks. |
| 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 |
| plotTrajectory | Visualize a Trajectory from ArchR Project |
| plotTrajectoryHeatmap | Plot a Heatmap of Features across a Trajectory |
| plotTSSEnrichment | Plot a TSS Enrichment Plot for Each Sample |
| projectBulkATAC | Project Bulk ATAC-seq data into single cell subspace |
-- R --
| recoverArchRProject | Recover ArchRProject if broken sampleColData/cellColData |
| reformatFragmentFiles | Reformat Fragment Files to be Tabix and Chr Sorted |
-- S --
| saveArchRProject | Save ArchRProject for Later Usage |
| setArchRLocking | Set a globally-applied H5 file locking setup |
| subsetArchRProject | Subset an ArchRProject for downstream analysis |
| subsetCells | Subset cells in an ArchRProject. |
-- T --
| theme_ArchR | ggplot2 default theme for ArchR |
-- V --
| validBSgenome | Get/Validate BSgenome |
-- misc --
| $.ArchRProject | Accessing cellColData directly from dollar.sign accessor |
| $<-.ArchRProject | Add directly to cellColData directly from dollar.sign accessor |
| %bcin% | Generic matching function for S4Vector objects |
| %bcni% | Negated matching function for S4Vector objects |
| %ni% | Negated Value Matching |
| .DollarNames.ArchRProject | Accessing cellColData directly from dollar.sign accessor |
| [.ArchRProject | Subset cells directly from ArchRProject |