Files in cole-trapnell-lab/monocle3
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md
.gitignore
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md R/RcppExports.R R/alignment.R R/cell_data_set.R R/cluster_cells.R R/cluster_genes.R R/expr_models.R R/find_markers.R R/generics.R R/graph_test.R R/learn_graph.R R/load_cellranger_data.R R/methods-cell_data_set.R R/order_cells.R R/plotting.R R/preprocess_cds.R R/reduce_dimensions.R R/select_cells.R R/utils.R README.md code-of-conduct.md examples/c_elegans_L2.R examples/c_elegans_embryo.R examples/website_script.R
inst/CITATION
inst/WORDLIST
inst/extdata/barcodes_c2h0.txt
inst/extdata/features_c3h0.txt
inst/extdata/lung_exprs_data.RData
inst/extdata/lung_feature_data.RData
inst/extdata/lung_phenotype_data.RData
inst/extdata/matrix.mtx.gz
inst/extdata/small_a549_dex_exprs.rda
inst/extdata/small_a549_dex_fdata.rda
inst/extdata/small_a549_dex_pdata.rda
inst/louvain.py
man/aggregate_gene_expression.Rd man/align_cds.Rd man/calc_principal_graph.Rd man/calculateLW.Rd man/cell_data_set-methods.Rd man/cell_data_set.Rd man/choose_cells.Rd man/choose_graph_segments.Rd man/clear_cds_slots.Rd man/cluster_cells.Rd man/clusters-cell_data_set-method.Rd man/clusters.Rd man/coefficient_table.Rd man/combine_cds.Rd man/compare_models.Rd man/detect_genes.Rd man/estimate_size_factors.Rd man/evaluate_fits.Rd man/exprs-cell_data_set-method.Rd man/exprs.Rd man/fData-cell_data_set-method.Rd man/fData-set-cell_data_set-method.Rd man/fData-set.Rd man/fData.Rd man/find_gene_modules.Rd man/find_nearest_vertex.Rd man/fit_model_helper.Rd man/fit_models.Rd man/generate_centers.Rd man/generate_garnett_marker_file.Rd man/get_citations.Rd man/get_genome_in_matrix_path.Rd man/graph_test.Rd man/learn_graph.Rd man/load_a549.Rd man/load_cellranger_data.Rd man/load_mm_data.Rd man/load_mtx_data.Rd man/load_worm_embryo.Rd man/mc_es_apply.Rd man/model_predictions.Rd man/my.aggregate.Matrix.Rd man/new_cell_data_set.Rd man/normalized_counts.Rd man/order_cells.Rd man/pData-cell_data_set-method.Rd man/pData-set-cell_data_set-method.Rd man/pData-set.Rd man/pData.Rd man/partitions-cell_data_set-method.Rd man/partitions.Rd man/plot_cells.Rd man/plot_cells_3d.Rd man/plot_genes_by_group.Rd man/plot_genes_in_pseudotime.Rd man/plot_genes_violin.Rd man/plot_pc_variance_explained.Rd man/plot_percent_cells_positive.Rd man/preprocess_cds.Rd man/principal_graph-cell_data_set-method.Rd man/principal_graph-set-cell_data_set-method.Rd man/principal_graph-set.Rd man/principal_graph.Rd man/principal_graph_aux-cell_data_set-method.Rd man/principal_graph_aux-set-cell_data_set-method.Rd man/principal_graph_aux-set.Rd man/principal_graph_aux.Rd man/pseudotime-cell_data_set-method.Rd man/pseudotime.Rd man/reduce_dimension.Rd man/repmat.Rd man/size_factors-set.Rd man/size_factors.Rd man/soft_assignment.Rd man/sparse_prcomp_irlba.Rd man/top_markers.Rd
monocle3.Rproj
src/.gitignore
src/Makevars
src/RcppExports.cpp
src/clustering.cpp
tests/spelling.R
tests/testdata/MatrixMarket/barcodes_c1h0.txt
tests/testdata/MatrixMarket/barcodes_c1h1.txt
tests/testdata/MatrixMarket/barcodes_c3h0.txt
tests/testdata/MatrixMarket/barcodes_c3h2.txt
tests/testdata/MatrixMarket/barcodes_c3h3.txt
tests/testdata/MatrixMarket/features_c1h0.txt
tests/testdata/MatrixMarket/features_c1h1.txt
tests/testdata/MatrixMarket/features_c2h1.txt
tests/testdata/MatrixMarket/features_c3h0.txt
tests/testdata/MatrixMarket/features_c3h2.txt
tests/testdata/MatrixMarket/features_c3h2q.txt
tests/testdata/MatrixMarket/features_c3h3.txt
tests/testdata/MatrixMarket/matrix.mtx.gz
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/test-alignment.R tests/testthat/test-cell_data_set.R tests/testthat/test-cluster_cells.R tests/testthat/test-cluster_genes.R tests/testthat/test-combine_cds.R tests/testthat/test-compare_models.R tests/testthat/test-evaluate_models.R tests/testthat/test-find_markers.R tests/testthat/test-fit_models.R tests/testthat/test-graph_test.R tests/testthat/test-learn_graph.R tests/testthat/test-load_cellranger_data.R tests/testthat/test-load_mm_data.R tests/testthat/test-order_cells.R tests/testthat/test-plotting.R tests/testthat/test-preprocessing.R tests/testthat/test-reduce_dimension.R tests/testthat/test-select_cells.R
vignettes/.gitignore
vignettes/monocle3-basics.Rmd
cole-trapnell-lab/monocle3 documentation built on April 8, 2021, 5:54 a.m.