Files in Bioconductor-mirror/monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/BEAM.R R/CellDataSet.R R/CellType.R R/CellTypeHierarchy.R R/clustering.R
R/data_sets.R
R/differential_expression.R R/expr_models.R R/methods-CellDataSet.R R/methods-CellTypeHierarchy.R R/normalization.R R/order_cells.R R/plotting.R R/utils.R
README
actual_vignette_holder/monocle-vignette-original.Rnw
data/spike_df.rda
examples/HSMM_analysis.R
inst/CITATION
inst/extdata/lung_exprs_data.RData
inst/extdata/lung_feature_data.RData
inst/extdata/lung_phenotype_data.RData
inst/tests/basic_tests.R inst/tests/test.dispersionTable.R inst/tests/test.estimateDispersions.R inst/tests/test.newCellDataSet.R inst/tests/test.newCellTypeHierarchy.R inst/tests/test.plotCellTrajectory.R man/BEAM.Rd man/CellDataSet-methods.Rd man/CellDataSet.Rd man/CellType.Rd man/CellTypeHierarchy.Rd man/branchTest.Rd man/buildBranchCellDataSet.Rd man/calABCs.Rd man/calILRs.Rd man/calibrate_per_cell_total_proposal.Rd man/cellPairwiseDistances-set.Rd man/cellPairwiseDistances.Rd man/clusterCells.Rd man/clusterGenes.Rd man/compareModels.Rd man/detectBifurcationPoint.Rd man/detectGenes.Rd man/diff_test_helper.Rd man/differentialGeneTest.Rd man/dispersionTable.Rd man/estimateDispersionsForCellDataSet.Rd man/estimateSizeFactorsForMatrix.Rd man/estimate_t.Rd man/extract_good_branched_ordering.Rd man/fitModel.Rd man/fit_model_helper.Rd man/genSmoothCurveResiduals.Rd man/genSmoothCurves.Rd man/get_classic_muscle_markers.Rd man/load_HSMM.Rd man/load_HSMM_markers.Rd man/load_lung.Rd man/markerDiffTable.Rd man/mcesApply.Rd man/minSpanningTree-set.Rd man/minSpanningTree.Rd man/newCellDataSet.Rd man/newCellTypeHierarchy.Rd man/orderCells.Rd man/order_p_node.Rd man/package-deprecated.Rd man/plot_cell_clusters.Rd man/plot_cell_trajectory.Rd man/plot_clusters.Rd man/plot_coexpression_matrix.Rd man/plot_complex_cell_trajectory.Rd man/plot_genes_branched_heatmap.Rd man/plot_genes_branched_pseudotime.Rd man/plot_genes_in_pseudotime.Rd man/plot_genes_jitter.Rd man/plot_genes_positive_cells.Rd man/plot_multiple_branches_heatmap.Rd man/plot_multiple_branches_pseudotime.Rd man/plot_ordering_genes.Rd man/plot_pc_variance_explained.Rd man/plot_pseudotime_heatmap.Rd man/plot_rho_delta.Rd man/pq_helper.Rd man/reduceDimension.Rd man/reducedDimA-set.Rd man/reducedDimA.Rd man/reducedDimK-set.Rd man/reducedDimK.Rd man/reducedDimS-set.Rd man/reducedDimS.Rd man/reducedDimW-set.Rd man/reducedDimW.Rd man/relative2abs.Rd man/residualMatrix.Rd man/responseMatrix.Rd man/selectNegentropyGenes.Rd man/selectTopMarkers.Rd man/setOrderingFilter.Rd man/spike_df.Rd man/vstExprs.Rd
monocle.Rproj
tests/testthat.R tests/testthat/test.BEAM.R tests/testthat/test.CellDataSet-setup.R tests/testthat/test.branchTest.R tests/testthat/test.buildLineageBranchCellDataSet.R tests/testthat/test.calIABCs.R tests/testthat/test.calILRs.R
tests/testthat/test.cellPairwiseDistances.R
tests/testthat/test.clusterCells.R tests/testthat/test.clusterGenes.R tests/testthat/test.compareModels.R tests/testthat/test.detectBifurcationPoint.R tests/testthat/test.detectGenes.R tests/testthat/test.differentialExpression.R tests/testthat/test.estimate_t.R tests/testthat/test.fitModels.R tests/testthat/test.genSmoothCurves.R tests/testthat/test.orderCells.R tests/testthat/test.reduceDimension.R tests/testthat/test.relative2abs.R tests/testthat/test.scale_pseudotime.R
vignettes/figure/check_clustering_again-1.png
vignettes/figure/check_clustering_again-2.png
vignettes/figure/check_the_clustering_results-1.png
vignettes/figure/check_the_clustering_results-2.png
vignettes/figure/cluster_cells_semisup_clustering_no_impute-1.png
vignettes/figure/cluster_cells_semisup_clustering_no_impute-2.png
vignettes/figure/cluster_cells_semisup_clustering_with_impute-1.png
vignettes/figure/cluster_cells_semisup_pick_genes-1.png
vignettes/figure/cluster_cells_unsup_control_for_media-1.png
vignettes/figure/cluster_cells_unsup_gene_pick-1.png
vignettes/figure/cluster_cells_unsup_no_covariate-1.png
vignettes/figure/cluster_cells_unsup_no_covariate-2.png
vignettes/figure/cluster_cells_unsup_plot_by_cell_type-1.png
vignettes/figure/cluster_cells_unsup_plot_by_media-1.png
vignettes/figure/count_cells_semisup_pie-1.png
vignettes/figure/count_cells_unsup_readout-1.png
vignettes/figure/init_hsmm_facet_state-1.png
vignettes/figure/init_hsmm_jitter_state-1.png
vignettes/figure/init_treutlein-1.png
vignettes/figure/jitter_plot_diff_res-1.png
vignettes/figure/lognormal_plot-1.png
vignettes/figure/lung_beam_branched_heatmap-1.png
vignettes/figure/lung_beam_branched_pseudotime-1.png
vignettes/figure/order_cells_dp_feature-1.png
vignettes/figure/order_cells_pca_unsup-1.png
vignettes/figure/plot_diff_res_multi-1.png
vignettes/figure/plot_diff_res_pt-1.png
vignettes/figure/plot_diff_res_pt_heatmap-1.png
vignettes/figure/plot_markers_linear-1.png
vignettes/figure/plot_myog_jitter-1.png
vignettes/figure/plot_ordering_mst-1.png
vignettes/figure/plot_ordering_mst_by_state-1.png
vignettes/figure/plot_ordering_with_GM_state-1.png
vignettes/figure/plot_pc_variance-1.png
vignettes/figure/plot_rho_delta-1.png
vignettes/figure/semi_sup_ordering_genes_in_pseudotime-1.png
vignettes/figure/semi_sup_ordering_trajectory-1.png
vignettes/figure/set_ordering_filter-1.png
vignettes/figure/show_mRNA_totals-1.png
vignettes/framed.sty
vignettes/monocle-vignette-knitr-concordance.tex
vignettes/monocle-vignette-knitr.bbl
vignettes/monocle-vignette-knitr.log
vignettes/monocle-vignette-knitr.pdf
vignettes/monocle-vignette-knitr.synctex.gz
vignettes/monocle-vignette-knitr.tex
vignettes/monocle-vignette-knitr.toc
vignettes/monocle-vignette.Rnw
vignettes/monocle_alg.bib
vignettes/whbiocvignette.sty
Bioconductor-mirror/monocle documentation built on Aug. 10, 2017, 10:49 a.m.