Files in monocle

Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

README.md R/methods-CellTypeHierarchy.R R/differential_expression.R R/CellDataSet.R R/RcppExports.R R/utils.R R/clustering.R R/data_sets.R R/expr_models.R R/plotting.R R/cds_conversion.R R/order_cells.R R/methods-CellDataSet.R R/normalization.R R/BEAM.R R/CellTypeHierarchy.R R/CellType.R vignettes/monocle-vignette-knitr.pdf examples/HSMM_analysis.R man/genSmoothCurves.Rd man/spike_df.Rd man/plot_pseudotime_heatmap.Rd man/order_p_node.Rd man/genSmoothCurveResiduals.Rd man/orderCells.Rd man/CellType.Rd man/reducedDimK.Rd man/importCDS.Rd man/plot_genes_jitter.Rd man/reducedDimS-set.Rd man/setOrderingFilter.Rd man/estimateSizeFactorsForMatrix.Rd man/branchTest.Rd man/get_classic_muscle_markers.Rd man/addCellType.Rd man/plot_multiple_branches_pseudotime.Rd man/compareModels.Rd man/detectGenes.Rd man/plot_pc_variance_explained.Rd man/plot_clusters.Rd man/newCellDataSet.Rd man/CellTypeHierarchy.Rd man/plot_cell_trajectory.Rd man/pq_helper.Rd man/reducedDimW.Rd man/newCellTypeHierarchy.Rd man/selectTopMarkers.Rd man/reducedDimA-set.Rd man/mcesApply.Rd man/plot_genes_violin.Rd man/load_lung.Rd man/cellPairwiseDistances.Rd man/fitModel.Rd man/fit_model_helper.Rd man/vstExprs.Rd man/plot_genes_branched_heatmap.Rd man/calABCs.Rd man/diff_test_helper.Rd man/minSpanningTree-set.Rd man/residualMatrix.Rd man/cellPairwiseDistances-set.Rd man/relative2abs.Rd man/minSpanningTree.Rd man/dispersionTable.Rd man/markerDiffTable.Rd man/responseMatrix.Rd man/calibrate_per_cell_total_proposal.Rd man/reducedDimW-set.Rd man/plot_multiple_branches_heatmap.Rd man/reduceDimension.Rd man/CellDataSet.Rd man/estimate_t.Rd man/plot_genes_branched_pseudotime.Rd man/clusterGenes.Rd man/CellDataSet-methods.Rd man/plot_cell_clusters.Rd man/calILRs.Rd man/buildBranchCellDataSet.Rd man/reducedDimK-set.Rd man/plot_coexpression_matrix.Rd man/plot_rho_delta.Rd man/plot_genes_positive_cells.Rd man/detectBifurcationPoint.Rd man/estimateDispersionsForCellDataSet.Rd man/BEAM.Rd man/plot_complex_cell_trajectory.Rd man/clusterCells.Rd man/reducedDimA.Rd man/reducedDimS.Rd man/differentialGeneTest.Rd man/exportCDS.Rd man/plot_ordering_genes.Rd man/extract_good_branched_ordering.Rd man/plot_genes_in_pseudotime.Rd man/load_HSMM_markers.Rd man/load_HSMM.Rd man/package-deprecated.Rd tests/testthat.R tests/testthat/test.plot_ordering_genes.R tests/testthat/test.orderCells.R tests/testthat/test.calculateMarkerSpecificity.R tests/testthat/test.classifyCells.R tests/testthat/test.detectGenes.R tests/testthat/test.plot_pc_variance_explained.R tests/testthat/test.newCellDataSet.R tests/testthat/test.addCellType.R tests/testthat/test.reduceDimension.R tests/testthat/test.plot_genes_jitter.R tests/testthat/test.differentialGeneTest.R tests/testthat/test.newCellTypeHierarchy.R tests/testthat/test.plot_cell_clusters.R tests/testthat/test.estimateDispersions.R tests/testthat/test.relative2abs.R tests/testthat/test.setOrderingFilter.R tests/testthat/test.dispersionTable.R tests/testthat/test.markerDiffTable.R tests/testthat/basic_tests.R tests/testthat/test.clusterCells.R tests/testthat/test.plotCellTrajectory.R inst/doc/monocle-vignette.R inst/doc/monocle-vignette.pdf inst/tests/test.plot_ordering_genes.R inst/tests/test.orderCells.R inst/tests/test.calculateMarkerSpecificity.R inst/tests/test.classifyCells.R inst/tests/test.detectGenes.R inst/tests/test.plot_pc_variance_explained.R inst/tests/test.newCellDataSet.R inst/tests/test.addCellType.R inst/tests/test.reduceDimension.R inst/tests/test.plot_genes_jitter.R inst/tests/test.differentialGeneTest.R inst/tests/test.newCellTypeHierarchy.R inst/tests/test.plot_cell_clusters.R inst/tests/test.estimateDispersions.R inst/tests/test.relative2abs.R inst/tests/test.setOrderingFilter.R inst/tests/test.dispersionTable.R inst/tests/test.markerDiffTable.R inst/tests/basic_tests.R inst/tests/test.clusterCells.R inst/tests/test.plotCellTrajectory.R