Files in MOCHA

Modeling for Single-Cell Open Chromatin Analysis

NEWS.md README.md R/plottingUtils.R R/getDifferentialAccessibleTiles.R R/runZIGLMM.R R/zi_spearman.R R/getCoverage.R R/getAltTSS.R R/models.R R/extractRegion.R R/singlePopulationSampleTileMatrix.R R/getPopFrags.R R/addAccessibilityShift.R R/MotifSetEnrichmentAnalysis.R R/getSampleTileMatrix.R R/testCoAccessibility.R R/annotateTiles.R R/make_prediction.R R/MotifEnrichment.R R/exportCoverage.R R/packMOCHA.R R/singlePopulationConsensusTiles.R R/calculate_intensities.R R/combineSampleTileMatrix.R R/runLMEM.R R/dimensionalityReduction.R R/mergeTileResults.R R/getCoAccessibleLinks.R R/plotConsensus.R R/heuristicAnalysis.R R/addMotifSet.R R/getCellPopMatrix.R R/co_accessibility.R R/callOpenTiles.R R/dynamic_bins.R R/filterCoAccessibleLinks.R R/exportSmoothedInsertions.R R/estimate_differential_accessibility.R R/two_part.R R/callTilesBySample.R R/plotRegion.R R/determine_dynamic_range.R R/varZIGLMM.R R/subsetMOCHAObject.R R/utils.R inst/doc/COVID-walkthrough.Rmd inst/doc/ImportingFromOtherSources.R inst/doc/COVID-walkthrough.R inst/doc/ImportingFromOtherSources.Rmd tests/testthat.R tests/testthat/test_COVID_data_pipeline.R tests/testthat/test_testCoAccessibility.R tests/testthat/test_combineSampleTileMatrix.R tests/testthat/test_MotifEnrichment.R tests/testthat/test_getAnnotationDbFromInstalledPkgname.R tests/testthat/test_exportCoverage.R tests/testthat/test_getPopFrags.R tests/testthat/test_subsetMOCHAObject.R tests/testthat/test_annotateTiles.R tests/testthat/test_getDifferentialAccessibleTiles.R tests/testthat/test_exportDifferentials.R tests/testthat/test_runLMEM.R tests/testthat/test_getSampleTileMatrix.R tests/testthat/test_plotRegion.R tests/testthat/test_extractRegion.R tests/testthat/test_packMOCHA.R tests/testthat/test_MotifSetEnrichmentAnalysis.R tests/testthat/setup.R tests/testthat/test_getCoverage.R tests/testthat/test_exportMotifs.R tests/testthat/test_exportOpenTiles.R tests/testthat/test_callOpenTiles.R tests/testthat/test_addMotifSet.R tests/testthat/test_dimensionalityReduction.R tests/testthat/test_getCoAccessibleLinks.R tests/testthat/_snaps/dimensionalityReduction.md tests/testthat/_snaps/MotifEnrichment.md tests/testthat/_snaps/getPopFrags.md tests/testthat/_snaps/getSampleTileMatrix.md tests/testthat/_snaps/extractRegion.md tests/testthat/_snaps/getCoverage.md tests/testthat/_snaps/nFrags/getPopFrags.md tests/testthat/_snaps/ArchR_metadata/callOpenTiles.md tests/testthat/_snaps/ArchR/callOpenTiles.md tests/testthat/_snaps/Median/getPopFrags.md tests/testthat/_snaps/raw/getPopFrags.md tests/testthat/_snaps/basic/getCoAccessibleLinks.md tests/testthat/_snaps/raw_sampleSpecific/getPopFrags.md tests/testthat/_snaps/nFrags_sampleSpecific/getPopFrags.md tests/testthat/_snaps/FragmentCounts/callOpenTiles.md tests/testthat/_snaps/tileResults/subsetMOCHAObject.md tests/testthat/_snaps/nrows/getCoAccessibleLinks.md tests/testthat/_snaps/CellCounts/callOpenTiles.md tests/testthat/_snaps/length/getDifferentialAccessibleTiles.md tests/testthat/_snaps/sampleTileMatrix_peaks/subsetMOCHAObject.md tests/testthat/_snaps/tiles/getCoAccessibleLinks.md tests/testthat/_snaps/tiles_3sample/getCoAccessibleLinks.md tests/testthat/_snaps/differentials/getDifferentialAccessibleTiles.md tests/testthat/_snaps/list/callOpenTiles.md tests/testthat/_snaps/3sample/combineSampleTileMatrix.md tests/testthat/_snaps/3sample/testCoAccessibility.md tests/testthat/_snaps/3sample/annotateTiles.md tests/testthat/_snaps/1sample/combineSampleTileMatrix.md tests/testthat/_snaps/1sample/testCoAccessibility.md tests/testthat/_snaps/1sample/annotateTiles.md tests/testthat/_snaps/list_metadata/callOpenTiles.md tests/testthat/_snaps/nrows_3sample/getCoAccessibleLinks.md tests/testthat/_snaps/sampleTileMatrix/subsetMOCHAObject.md tests/testthat/_snaps/Median_sampleSpecific/getPopFrags.md tests/testthat/_snaps/nCells_sampleSpecific/getPopFrags.md tests/testthat/_snaps/nCells/getPopFrags.md vignettes/COVID-walkthrough.Rmd vignettes/ImportingFromOtherSources.Rmd man/getSampleTileMatrix.Rd man/extractErrorFromConsensusTiles.Rd man/varZIGLMM.Rd man/MotifSetEnrichmentAnalysis.Rd man/getCellTypes.Rd man/unpackMOCHA.Rd man/exportCoverage.Rd man/exampleFragments.Rd man/runZIGLMM.Rd man/exportMotifs.Rd man/getIntensityThreshold.Rd man/testCoAccessibilityRandom.Rd man/mergeTileResults.Rd man/getModelValues.Rd man/addAccessibilityShift.Rd man/bulkDimReduction.Rd man/differentialsToGRanges.Rd man/testCoAccessibilityChromVar.Rd man/pilotLMEM.Rd man/subsetMOCHAObject.Rd man/annotateTiles.Rd man/youden_threshold.Rd man/singlePopulationSampleTileMatrix.Rd man/exampleCellColData.Rd man/testCoAccessibility.Rd man/bulkUMAP.Rd man/getCellPopMatrix.Rd man/getSampleCellTypeMetadata.Rd man/pilotZIGLMM.Rd man/getCoverage.Rd man/dot-counts_plot_default_theme.Rd man/plotRegion.Rd man/dot-gene_plot_theme.Rd man/simplifiedConsensusTiles.Rd man/exportDifferentials.Rd man/extractRegion.Rd man/runLMEM.Rd man/getDifferentialAccessibleTiles.Rd man/getPopFrags.Rd man/filterCoAccessibleLinks.Rd man/exportSmoothedInsertions.Rd man/callOpenTiles-methods.Rd man/getCoAccessibleLinks.Rd man/getCellTypeTiles.Rd man/MotifEnrichment.Rd man/plotConsensus.Rd man/packMOCHA.Rd man/getSequencingBias.Rd man/finalModelObject.Rd man/getAltTSS.Rd man/combineSampleTileMatrix.Rd man/exportOpenTiles.Rd man/exampleBlackList.Rd man/GRangesToString.Rd man/renameCellTypes.Rd man/singlePopulationConsensusTiles.Rd man/StringsToGRanges.Rd man/getPromoterGenes.Rd man/plotIntensityDistribution.Rd man/getAnnotationDbFromInstalledPkgname.Rd man/addMotifSet.Rd