Files in cole-trapnell-lab/monocle-release
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/BEAM.R
R/CellDataSet.R
R/CellType.R
R/CellTypeHierarchy.R
R/RcppExports.R
R/cds_conversion.R
R/clustering.R
R/data_io.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.md
actual_vignette_holder/monocle-vignette-knitr.bbl
actual_vignette_holder/monocle-vignette-original.Rnw
data/spike_df.rda
examples/HSMM_analysis.R
inst/CITATION
inst/doc/monocle-vignette.R
inst/doc/monocle-vignette.Rnw
inst/doc/monocle-vignette.pdf
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.addCellType.R
inst/tests/test.calculateMarkerSpecificity.R
inst/tests/test.classifyCells.R
inst/tests/test.clusterCells.R
inst/tests/test.detectGenes.R
inst/tests/test.differentialGeneTest.R
inst/tests/test.dispersionTable.R
inst/tests/test.estimateDispersions.R
inst/tests/test.markerDiffTable.R
inst/tests/test.newCellDataSet.R
inst/tests/test.newCellTypeHierarchy.R
inst/tests/test.orderCells.R
inst/tests/test.plotCellTrajectory.R
inst/tests/test.plot_cell_clusters.R
inst/tests/test.plot_genes_jitter.R
inst/tests/test.plot_ordering_genes.R
inst/tests/test.plot_pc_variance_explained.R
inst/tests/test.reduceDimension.R
inst/tests/test.relative2abs.R
inst/tests/test.setOrderingFilter.R
man/BEAM.Rd
man/CellDataSet-methods.Rd
man/CellDataSet.Rd
man/CellType.Rd
man/CellTypeHierarchy.Rd
man/addCellType.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/exportCDS.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/importCDS.Rd
man/load_HSMM.Rd
man/load_HSMM_markers.Rd
man/load_cellranger_data.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_genes_violin.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/selectTopMarkers.Rd
man/setOrderingFilter.Rd
man/spike_df.Rd
man/vstExprs.Rd
monocle.Rproj
src/.gitignore
src/RcppExports.cpp
src/clustering.cpp
tests/testdata/cr2.0/outs/filtered_gene_bc_matrices/hg19/barcodes.tsv
tests/testdata/cr2.0/outs/filtered_gene_bc_matrices/hg19/genes.tsv
tests/testdata/cr2.0/outs/filtered_gene_bc_matrices/hg19/matrix.mtx
tests/testdata/cr3.0/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
tests/testdata/cr3.0/outs/filtered_feature_bc_matrix/features.tsv.gz
tests/testdata/cr3.0/outs/filtered_feature_bc_matrix/matrix.mtx.gz
tests/testthat.R
tests/testthat/basic_tests.R
tests/testthat/test.addCellType.R
tests/testthat/test.calculateMarkerSpecificity.R
tests/testthat/test.classifyCells.R
tests/testthat/test.clusterCells.R
tests/testthat/test.detectGenes.R
tests/testthat/test.differentialGeneTest.R
tests/testthat/test.dispersionTable.R
tests/testthat/test.estimateDispersions.R
tests/testthat/test.markerDiffTable.R
tests/testthat/test.newCellDataSet.R
tests/testthat/test.newCellTypeHierarchy.R
tests/testthat/test.orderCells.R
tests/testthat/test.plotCellTrajectory.R
tests/testthat/test.plot_cell_clusters.R
tests/testthat/test.plot_genes_jitter.R
tests/testthat/test.plot_ordering_genes.R
tests/testthat/test.plot_pc_variance_explained.R
tests/testthat/test.reduceDimension.R
tests/testthat/test.relative2abs.R
tests/testthat/test.setOrderingFilter.R
tests/testthat/test_load_10X.R
travis_setup.sh
vignettes/figure/gene_pairwise_kinetic_plot-1.png
vignettes/framed.sty
vignettes/monocle-vignette-knitr-concordance.tex
vignettes/monocle-vignette-knitr.pdf
vignettes/monocle-vignette-knitr.synctex.gz
vignettes/monocle-vignette-knitr.tex
vignettes/monocle-vignette.Rnw
vignettes/monocle-vignette.pdf
vignettes/monocle_alg.bib
vignettes/whbiocvignette.sty
