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:
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)
NEWS
# Install 'MOCHA' in R: |
install.packages('MOCHA', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- exampleBlackList - ExampleBlackList
- exampleCellColData - ExampleCellColData
- exampleFragments - ExampleFragments
- finalModelObject - FinalModelObject
- youden_threshold - Youden_threshold
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 months agofrom:7f9d172bfc. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 21 2024 |
R-4.5-linux | OK | Dec 21 2024 |
Exports:addAccessibilityShiftaddMotifSetannotateTilesbulkDimReductionbulkUMAPcallOpenTilescombineSampleTileMatrixdifferentialsToGRangesexportCoverageexportDifferentialsexportMotifsexportOpenTilesexportSmoothedInsertionsextractRegionfilterCoAccessibleLinksgetAltTSSgetCellPopMatrixgetCellTypesgetCellTypeTilesgetCoAccessibleLinksgetCoveragegetDifferentialAccessibleTilesgetModelValuesgetPopFragsgetPromoterGenesgetSampleCellTypeMetadatagetSampleTileMatrixGRangesToStringmergeTileResultsMotifEnrichmentMotifSetEnrichmentAnalysispackMOCHApilotLMEMpilotZIGLMMplotConsensusplotIntensityDistributionplotRegionrenameCellTypesrunLMEMrunZIGLMMStringsToGRangessubsetMOCHAObjecttestCoAccessibilitytestCoAccessibilityChromVartestCoAccessibilityRandomunpackMOCHAvarZIGLMM
Dependencies:abindAnnotationDbiAnnotationFilteraskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggplot2ggrepelggridgesggstatsgluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamnormtMultiAssayExperimentmunsellnlmennetopensslOrganismDbipatchworkpbapplypillarpkgconfigplogrplyrplyrangespngprettyunitsprogressProtGenericspurrrqvalueR6RaggedExperimentrappdirsRBGLRColorBrewerRcppRcppArmadilloRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewCorrwithrxfunXMLxml2XVectoryamlzlibbioc