Package: ArchR 1.0.2

Jeffrey Granja

ArchR: Analyzing single-cell regulatory chromatin in R.

This package is designed to streamline scATAC analyses in R.

Authors:Jeffrey Granja [aut, cre], Ryan Corces [aut]

ArchR_1.0.2.tar.gz
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ArchR.pdf |ArchR.html
ArchR/json (API)

# Install 'ArchR' in R:
install.packages('ArchR', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/greenleaflab/archr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

    On CRAN:

    155 exports 360 stars 6.56 score 177 dependencies

    Last updated 5 months agofrom:d9e741c980

    Exports:.DollarNames.ArchRProject%bcin%%bcni%%ni%addArchRAnnotationsaddArchRChrPrefixaddArchRDebuggingaddArchRGenomeaddArchRLoggingaddArchRThreadsaddArchRVerboseaddBgdPeaksaddCellColDataaddClustersaddCoAccessibilityaddCombinedDimsaddDemuxletResultsaddDeviationsMatrixaddDoubletScoresaddFeatureCountsaddFeatureMatrixaddGeneExpressionMatrixaddGeneIntegrationMatrixaddGeneScoreMatrixaddGroupCoveragesaddHarmonyaddImputeWeightsaddIterativeLSIaddModuleScoreaddMonocleTrajectoryaddMotifAnnotationsaddPeak2GeneLinksaddPeakAnnotationsaddPeakMatrixaddPeakSetaddProjectSummaryaddReproduciblePeakSetaddSampleColDataaddSlingShotTrajectoriesaddTileMatrixaddTrajectoryaddTSNEaddUMAPArchRBrowserArchRBrowserTrackArchRPalettesArchRProjectconfusionMatrixcorrelateMatricescorrelateTrajectoriescreateArrowFilescreateGeneAnnotationcreateGenomeAnnotationcreateLogFileenrichHeatmapexportGroupSEexportPeakMatrixForSTREAMextendGRfilterChrGRfilterDoubletsfindMacs2getArchRChrPrefixgetArchRDebugginggetArchRGenomegetArchRLogginggetArchRThreadsgetArchRVerbosegetArrowFilesgetAvailableMatricesgetBgdPeaksgetBlacklistgetCellColDatagetCellNamesgetChromLengthsgetChromSizesgetCoAccessibilitygetEmbeddinggetExonsgetFeaturesgetFootprintsgetFragmentsFromArrowgetFragmentsFromProjectgetGeneAnnotationgetGenesgetGenomegetGenomeAnnotationgetGroupBWgetGroupSEgetGroupSummarygetImputeWeightsgetInputFilesgetMarkerFeaturesgetMarkersgetMatchesgetMatrixFromArrowgetMatrixFromProjectgetMonocleTrajectoriesgetOutputDirectorygetPeak2GeneLinksgetPeakAnnotationgetPeakSetgetPositionsgetProjectSummarygetReducedDimsgetSampleColDatagetSampleNamesgetSeqnamesgetTestFragmentsgetTestProjectgetTrajectorygetTSSgetTutorialDatagetValidBarcodesgetVarDeviationsggAlignPlotsggGroupggHexggOneToOneggPointimport10xFeatureMatriximputeMatrixinstallExtraPackagesloadArchRProjectmapLabelsmarkerFeaturesmarkerHeatmapmarkerPlotnCellsnonOverlappingGRpaletteContinuouspaletteDiscretepeak2GeneHeatmappeakAnnoEnrichmentplotBrowserTrackplotEmbeddingplotEnrichHeatmapplotFootprintsplotFragmentSizesplotGroupsplotMarkerHeatmapplotMarkersplotPDFplotPeak2GeneHeatmapplotTrajectoryplotTrajectoryHeatmapplotTSSEnrichmentprojectBulkATACrecoverArchRProjectreformatFragmentFilessaveArchRProjectsubsetArchRProjectsubsetCellstheme_ArchRtrajectoryHeatmapvalidBSgenome

    Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcaToolschromVARcirclizeclicliprclueclusterCNErcodetoolscolorspacecommonmarkComplexHeatmapcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestDirichletMultinomialdoParalleldplyrdqrngDTevaluatefansifarverfastmapFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsglueGO.dbgridExtragtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImotifmatchrmunsellnabornlmeopensslpillarpkgconfigplogrplotlyplyrpngpoweRlawpracmaprettyunitsprogresspromisespurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRCurlreadrreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSpectraRSQLitertracklayerRtsneS4ArraysS4VectorssassscalesseqLogoshapeshinysitmosnowsourcetoolsSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8uwotvctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioc

    Readme and manuals

    Help Manual

    Help pageTopics
    Accessing cellColData directly from dollar.sign accessor.DollarNames.ArchRProject
    Subset cells directly from ArchRProject[.ArchRProject
    Generic matching function for S4Vector objects%bcin%
    Negated matching function for S4Vector objects%bcni%
    Negated Value Matching%ni%
    Accessing cellColData directly from dollar.sign accessor$.ArchRProject
    Add directly to cellColData directly from dollar.sign accessor$<-.ArchRProject
    Add ArchR annotations to an ArchRProjectaddArchRAnnotations
    Add a globally-applied requirement for chromosome prefixaddArchRChrPrefix
    Set ArchR DebuggingaddArchRDebugging
    Add a globally defined genome to all ArchR functions.addArchRGenome
    Set ArchR LoggingaddArchRLogging
    Add a globally-applied number of threads to use for parallel computing.addArchRThreads
    Set ArchR Verbosity for Log MessagingaddArchRVerbose
    Add Background Peaks to an ArchRProjectaddBgdPeaks
    Add information to cellColData in an ArchRProjectaddCellColData
    Add cluster information to an ArchRProjectaddClusters
    Add Peak Co-Accessibility to an ArchRProjectaddCoAccessibility
    Combine two or more modalities dimensionality reductions.addCombinedDims
    Add Demuxlet Results to ArchR ProjectaddDemuxletResults
    Add a matrix of deviations for a given peakAnnotation to Arrow Files in ArchRProjectaddDeviationsMatrix
    Add Doublet Scores to a collection of ArrowFiles or an ArchRProjectaddDoubletScores
    This function will add total counts of scATAC cells in provided features into ArchRProject.addFeatureCounts
    Add a feature matrix to an ArchRProject or a set of ArrowFilesaddFeatureMatrix
    Add Gene Expression Matrix to ArrowFiles or an ArchRProjectaddGeneExpressionMatrix
    Add a GeneIntegrationMatrix to ArrowFiles or an ArchRProjectaddGeneIntegrationMatrix
    Add GeneScoreMatrix to ArrowFiles or an ArchRProjectaddGeneScoreMatrix
    Add Group Coverages to an ArchRProject objectaddGroupCoverages
    Add Harmony Batch Corrected Reduced Dims to an ArchRProjectaddHarmony
    Add Imputation Weights to an ArchRProjectaddImputeWeights
    Add an Iterative LSI-based dimensionality reduction to an ArchRProjectaddIterativeLSI
    Add Module Scores to an ArchRProjectaddModuleScore
    Add a Monocle Trajectory to an ArchR Project #NEWaddMonocleTrajectory
    Add motif annotations to an ArchRProjectaddMotifAnnotations
    Add Peak2GeneLinks to an ArchRProjectaddPeak2GeneLinks
    Add peak annotations to an ArchRProjectaddPeakAnnotations
    Add a Peak Matrix to the ArrowFiles of an ArchRProjectaddPeakMatrix
    Add a peak set to an ArchRProjectaddPeakSet
    Add projectSummary to an ArchRProjectaddProjectSummary
    Add a Reproducible Peak Set to an ArchRProjectaddReproduciblePeakSet
    Add information to sampleColData in an ArchRProjectaddSampleColData
    Add a Slingshot Trajectories to an ArchR Project #NEWaddSlingShotTrajectories
    Add TileMatrix to ArrowFiles or an ArchRProjectaddTileMatrix
    Add a Supervised Trajectory to an ArchR ProjectaddTrajectory
    Add a TSNE embedding of a reduced dimensions object to an ArchRProjectaddTSNE
    Add a UMAP embedding of a reduced dimensions object to an ArchRProjectaddUMAP
    Launch ArchR Genome BrowserArchRBrowser
    List of color palettes that can be used in plotsArchRPalettes
    Create ArchRProject from ArrowFilesArchRProject
    Create a Confusion Matrix based on two value vectorsconfusionMatrix
    Correlate Matrices within an ArchRProjectcorrelateMatrices
    Correlate TrajectoriescorrelateTrajectories
    Create Arrow FilescreateArrowFiles
    Create a gene annotation object for ArchRcreateGeneAnnotation
    Create a genome annotation object for ArchRcreateGenomeAnnotation
    Create a Log File for ArchRcreateLogFile
    Get a PeakMatrix stored in an ArchRProject and write out for STREAMexportPeakMatrixForSTREAM
    Extend regions from a Genomic Ranges objectextendGR
    Filters unwanted seqlevels from a Genomic Ranges object or similar objectfilterChrGR
    Filter Doublets From an ArchRProjectfilterDoublets
    Find the installed location of the MACS2 executablefindMacs2
    Get a globally-applied requirement for chromosome prefixgetArchRChrPrefix
    Get ArchR DebugginggetArchRDebugging
    Get the globally defined genome, the geneAnnotation, or genomeAnnotation objects associated with the globally defined genome.getArchRGenome
    Get ArchR LogginggetArchRLogging
    Get globally-applied number of threads to use for parallel computing.getArchRThreads
    Set ArchR Verbosity for Log MessaginggetArchRVerbose
    Get ArrowFiles from an ArchRProjectgetArrowFiles
    Get a list available matrices in the ArrowFiles storted in an ArchRProjectgetAvailableMatrices
    Get Background Peaks from an ArchRProjectgetBgdPeaks
    Get the blacklist from an ArchRProjectgetBlacklist
    Get cellColData from an ArchRProjectgetCellColData
    Get cellNames from an ArchRProjectgetCellNames
    Get chromLengths from ArchRProjectgetChromLengths
    Get chromSizes from ArchRProjectgetChromSizes
    Get the peak co-accessibility from an ArchRProjectgetCoAccessibility
    Get embedding information stored in an ArchRProjectgetEmbedding
    Get the exons from an ArchRProjectgetExons
    Get the features that could be selected from a given data matrix within an ArchRProjectgetFeatures
    Calculate footprints from an ArchRProjectgetFootprints
    Get the fragments from an ArrowFilegetFragmentsFromArrow
    Get the fragments from an ArchRProjectgetFragmentsFromProject
    Get geneAnnotation from an ArchRProjectgetGeneAnnotation
    Get the genes from an ArchRProjectgetGenes
    Get the genome used by an ArchRProjectgetGenome
    Get the genomeAnnotation from an ArchRProjectgetGenomeAnnotation
    Export Group BigWigsgetGroupBW
    Export Group Summarized ExperimentgetGroupSE
    Get summary for Groups in ArchRProjectgetGroupSummary
    Get Imputation Weights from ArchRProjectgetImputeWeights
    Get Input Files from paths to create arrowsgetInputFiles
    Identify Marker Features for each cell groupinggetMarkerFeatures
    Get Marker Features from a marker summarized experimentgetMarkers
    Get peak annotation matches from an ArchRProjectgetMatches
    Get a data matrix stored in an ArrowFilegetMatrixFromArrow
    Get a data matrix stored in an ArchRProjectgetMatrixFromProject
    Get a Monocle CDS of Trajectories that can be added to an ArchRProject #NEWgetMonocleTrajectories
    Get outputDirectory from an ArchRProjectgetOutputDirectory
    Get the peak-to-gene links from an ArchRProjectgetPeak2GeneLinks
    Get peakAnnotation from an ArchRProjectgetPeakAnnotation
    Get the peak set from an ArchRProjectgetPeakSet
    Get peak annotation positions from an ArchRProjectgetPositions
    Get projectSummary from an ArchRProjectgetProjectSummary
    Get dimensionality reduction information stored in an ArchRProjectgetReducedDims
    Get sampleColData from an ArchRProjectgetSampleColData
    Get the sample names from an ArchRProjectgetSampleNames
    Get the seqnames that could be selected from a given data matrix within an ArchRProjectgetSeqnames
    Get PBMC Small Test FragmentsgetTestFragments
    Get PBMC Small Test ProjectgetTestProject
    Get Supervised Trajectory from an ArchR ProjectgetTrajectory
    Get the transcription start sites of all genes in an ArchRProjectgetTSS
    Get Relevant Data For ArchR TutorialsgetTutorialData
    Get Valid Barcodes from 10x Cell Ranger output to pre-filter barcodesgetValidBarcodes
    Get Variable Deviations across cells in ArchRProject.getVarDeviations
    Align ggplot plots vertically or horizontallyggAlignPlots
    A ggplot-based ridge/violin plot wrapper functionggGroup
    A ggplot-based Hexplot wrapper function summary of points in a standardized mannerggHex
    A ggplot-based one-to-one dot plot wrapper functionggOneToOne
    A ggplot-based dot plot wrapper functionggPoint
    Import Feature Matrix from 10x Feature HDF5 file.import10xFeatureMatrix
    Impute a matrix with impute weightsimputeMatrix
    Install extra packages used in ArchR that are not installed by defaultinstallExtraPackages
    Load Previous ArchRProject into RloadArchRProject
    Re-map a character vector of labels from an old set of labels to a new set of labelsmapLabels
    Get the number of cells from an ArchRProject/ArrowFilenCells
    Retreive a non-overlapping set of regions from a Genomic Ranges objectnonOverlappingGR
    Continuous Color PalettepaletteContinuous
    Optimized discrete color palette generationpaletteDiscrete
    Peak Annotation Hypergeometric Enrichment in Marker Peaks.peakAnnoEnrichment
    Plot an ArchR Region TrackplotBrowserTrack
    Visualize an Embedding from ArchR ProjectplotEmbedding
    Plot a Heatmap of Peak Annotation Hypergeometric Enrichment in Marker Peaks.plotEnrichHeatmap
    Plot FootprintsplotFootprints
    Plot the fragment size distribution for each sampleplotFragmentSizes
    Visualize Groups from ArchR ProjectplotGroups
    Plot a Heatmap of Identified Marker FeaturesplotMarkerHeatmap
    Plot Differential MarkersplotMarkers
    Plot PDF in outputDirectory of an ArchRProjectplotPDF
    Plot Peak2Gene Heatmap from an ArchRProjectplotPeak2GeneHeatmap
    Visualize a Trajectory from ArchR ProjectplotTrajectory
    Plot a Heatmap of Features across a TrajectoryplotTrajectoryHeatmap
    Plot a TSS Enrichment Plot for Each SampleplotTSSEnrichment
    Project Bulk ATAC-seq data into single cell subspaceprojectBulkATAC
    Recover ArchRProject if broken sampleColData/cellColDatarecoverArchRProject
    Reformat Fragment Files to be Tabix and Chr SortedreformatFragmentFiles
    Save ArchRProject for Later UsagesaveArchRProject
    Subset an ArchRProject for downstream analysissubsetArchRProject
    Subset cells in an ArchRProject.subsetCells
    ggplot2 default theme for ArchRtheme_ArchR
    Get/Validate BSgenomevalidBSgenome