Package: ArchR 1.0.2
ArchR: Analyzing single-cell regulatory chromatin in R.
This package is designed to streamline scATAC analyses in R.
Authors:
ArchR_1.0.2.tar.gz
ArchR_1.0.2.zip(r-4.5)ArchR_1.0.2.zip(r-4.4)ArchR_1.0.2.zip(r-4.3)
ArchR_1.0.2.tgz(r-4.4-x86_64)ArchR_1.0.2.tgz(r-4.4-arm64)ArchR_1.0.2.tgz(r-4.3-x86_64)ArchR_1.0.2.tgz(r-4.3-arm64)
ArchR_1.0.2.tar.gz(r-4.5-noble)ArchR_1.0.2.tar.gz(r-4.4-noble)
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')) |
Bug tracker:https://github.com/greenleaflab/archr/issues
Last updated 7 months agofrom:d9e741c980. Checks:OK: 1 WARNING: 8. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 24 2024 |
R-4.5-win-x86_64 | WARNING | Aug 24 2024 |
R-4.5-linux-x86_64 | WARNING | Aug 24 2024 |
R-4.4-win-x86_64 | WARNING | Aug 24 2024 |
R-4.4-mac-x86_64 | WARNING | Aug 24 2024 |
R-4.4-mac-aarch64 | WARNING | Aug 24 2024 |
R-4.3-win-x86_64 | WARNING | Aug 24 2024 |
R-4.3-mac-x86_64 | WARNING | Aug 24 2024 |
R-4.3-mac-aarch64 | WARNING | Jul 25 2024 |
Exports:.DollarNames.ArchRProject%bcin%%bcni%%ni%addArchRAnnotationsaddArchRChrPrefixaddArchRDebuggingaddArchRGenomeaddArchRLoggingaddArchRThreadsaddArchRVerboseaddBgdPeaksaddCellColDataaddClustersaddCoAccessibilityaddCombinedDimsaddDemuxletResultsaddDeviationsMatrixaddDoubletScoresaddFeatureCountsaddFeatureMatrixaddGeneExpressionMatrixaddGeneIntegrationMatrixaddGeneScoreMatrixaddGroupCoveragesaddHarmonyaddImputeWeightsaddIterativeLSIaddModuleScoreaddMonocleTrajectoryaddMotifAnnotationsaddPeak2GeneLinksaddPeakAnnotationsaddPeakMatrixaddPeakSetaddProjectSummaryaddReproduciblePeakSetaddSampleColDataaddSlingShotTrajectoriesaddTileMatrixaddTrajectoryaddTSNEaddUMAPArchRBrowserArchRBrowserTrackArchRPalettesArchRProjectconfusionMatrixcorrelateMatricescorrelateTrajectoriescreateArrowFilescreateGeneAnnotationcreateGenomeAnnotationcreateLogFileenrichHeatmapexportGroupSEexportPeakMatrixForSTREAMextendGRfilterChrGRfilterDoubletsfindMacs2getArchRChrPrefixgetArchRDebugginggetArchRGenomegetArchRLogginggetArchRThreadsgetArchRVerbosegetArrowFilesgetAvailableMatricesgetBgdPeaksgetBlacklistgetCellColDatagetCellNamesgetChromLengthsgetChromSizesgetCoAccessibilitygetEmbeddinggetExonsgetFeaturesgetFootprintsgetFragmentsFromArrowgetFragmentsFromProjectgetGeneAnnotationgetGenesgetGenomegetGenomeAnnotationgetGroupBWgetGroupSEgetGroupSummarygetImputeWeightsgetInputFilesgetMarkerFeaturesgetMarkersgetMatchesgetMatrixFromArrowgetMatrixFromProjectgetMonocleTrajectoriesgetOutputDirectorygetPeak2GeneLinksgetPeakAnnotationgetPeakSetgetPositionsgetProjectSummarygetReducedDimsgetSampleColDatagetSampleNamesgetSeqnamesgetTestFragmentsgetTestProjectgetTrajectorygetTSSgetTutorialDatagetValidBarcodesgetVarDeviationsggAlignPlotsggGroupggHexggOneToOneggPointimport10xFeatureMatriximputeMatrixinstallExtraPackagesloadArchRProjectmapLabelsmarkerFeaturesmarkerHeatmapmarkerPlotnCellsnonOverlappingGRpaletteContinuouspaletteDiscretepeak2GeneHeatmappeakAnnoEnrichmentplotBrowserTrackplotEmbeddingplotEnrichHeatmapplotFootprintsplotFragmentSizesplotGroupsplotMarkerHeatmapplotMarkersplotPDFplotPeak2GeneHeatmapplotTrajectoryplotTrajectoryHeatmapplotTSSEnrichmentprojectBulkATACrecoverArchRProjectreformatFragmentFilessaveArchRProjectsubsetArchRProjectsubsetCellstheme_ArchRtrajectoryHeatmapvalidBSgenome
Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcaToolschromVARcirclizeclicliprclueclusterCNErcodetoolscolorspacecommonmarkComplexHeatmapcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestDirichletMultinomialdoParalleldplyrdqrngDTevaluatefansifarverfastmapFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsglueGO.dbgridExtragtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImotifmatchrmunsellnabornlmeopensslpillarpkgconfigplogrplotlyplyrpngpoweRlawpracmaprettyunitsprogresspromisespurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRCurlreadrreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSpectraRSQLitertracklayerRtsneS4ArraysS4VectorssassscalesseqLogoshapeshinysitmosnowsourcetoolsSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8uwotvctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioc