Package: MOCHA 1.1.0

Imran McGrath

MOCHA: Modeling for Single-Cell Open Chromatin Analysis

A statistical framework and analysis tool for open chromatin analysis designed specifically for single cell ATAC-seq (Assay for Transposase-Accessible Chromatin) data, after cell type/cluster identification. These novel modules remove unwanted technical variation, identify open chromatin, robustly models repeated measures in single cell data, implement advanced statistical frameworks to model zero-inflation for differential and co-accessibility analyses, and integrate with existing databases and modules for downstream analyses to reveal biological insights. MOCHA provides a statistical foundation for complex downstream analysis to help advance the potential of single cell ATAC-seq for applied studies. Methods for zero-inflated statistics are as described in: Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>. Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.

Authors:Samir Rachid Zaim [aut, ctb], Mark-Phillip Pebworth [aut, ctb], Imran McGrath [aut, cre], Lauren Okada [aut, ctb], Xiaojun Li [aut, ctb]

MOCHA_1.1.0.tar.gz
MOCHA_1.1.0.tar.gz(r-4.5-noble)MOCHA_1.1.0.tar.gz(r-4.4-noble)
MOCHA_1.1.0.tgz(r-4.4-emscripten)MOCHA_1.1.0.tgz(r-4.3-emscripten)
MOCHA.pdf |MOCHA.html✨
MOCHA/json (API)
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47 exports 0.36 score 174 dependencies 28 scripts 244 downloads

Last updated 8 months agofrom:7f9d172bfc. Checks:OK: 2. Indexed: yes.

Exports:addAccessibilityShiftaddMotifSetannotateTilesbulkDimReductionbulkUMAPcallOpenTilescombineSampleTileMatrixdifferentialsToGRangesexportCoverageexportDifferentialsexportMotifsexportOpenTilesexportSmoothedInsertionsextractRegionfilterCoAccessibleLinksgetAltTSSgetCellPopMatrixgetCellTypesgetCellTypeTilesgetCoAccessibleLinksgetCoveragegetDifferentialAccessibleTilesgetModelValuesgetPopFragsgetPromoterGenesgetSampleCellTypeMetadatagetSampleTileMatrixGRangesToStringmergeTileResultsMotifEnrichmentMotifSetEnrichmentAnalysispackMOCHApilotLMEMpilotZIGLMMplotConsensusplotIntensityDistributionplotRegionrenameCellTypesrunLMEMrunZIGLMMStringsToGRangessubsetMOCHAObjecttestCoAccessibilitytestCoAccessibilityChromVartestCoAccessibilityRandomunpackMOCHAvarZIGLMM

Dependencies:abindAnnotationDbiAnnotationFilteraskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbroombroom.helpersBSgenomebslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggplot2ggrepelggridgesggstatsgluegraphgridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglabelledlambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamnormtMultiAssayExperimentmunsellnlmennetopensslOrganismDbipatchworkpbapplypillarpkgconfigplogrplyrplyrangespngprettyunitsprogressProtGenericspurrrqvalueR6RaggedExperimentrappdirsRBGLRColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwCorrwithrxfunXMLxml2XVectoryamlzlibbioc