Files in keyes-timothy/tidytof

Analyze High-dimensional Cytometry Data Using Tidy Data Principles

.github/CODE_OF_CONDUCT.md .github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/issue_template.md LICENSE.md NEWS.md R/RcppExports.R R/batch_correction.R R/clustering.R R/data.R R/developmental_classifier_helpers.R R/differential_discovery.R R/dimensionality_reduction.R R/downsampling.R R/feature_extraction.R R/flowsom_metacluster_helpers.R R/imports.R R/io.R R/metaclustering.R R/modeling_helpers.R R/patient-level_modeling.R R/phenograph_helpers.R R/preprocessing.R R/quality_control.R R/tidytof-package.R R/tof_tbl.R R/upsample.R R/utils.R R/visualization.R README.Rmd README.md man/as_SingleCellExperiment.Rd man/as_flowFrame.Rd man/as_flowSet.Rd man/as_seurat.Rd man/as_tof_tbl.Rd man/as_tof_tbl.flowSet.Rd man/cosine_similarity.Rd man/ddpr_data.Rd man/ddpr_metadata.Rd man/dot.Rd man/get_extension.Rd man/l2_normalize.Rd man/magnitude.Rd man/make_flowcore_annotated_data_frame.Rd man/metal_masterlist.Rd man/new_tof_model.Rd man/new_tof_tibble.Rd man/phenograph_data.Rd man/reexports.Rd man/rev_asinh.Rd man/tidytof_example_data.Rd man/tof_analyze_abundance.Rd man/tof_analyze_abundance_diffcyt.Rd man/tof_analyze_abundance_glmm.Rd man/tof_analyze_abundance_ttest.Rd man/tof_analyze_expression.Rd man/tof_analyze_expression_diffcyt.Rd man/tof_analyze_expression_lmm.Rd man/tof_analyze_expression_ttest.Rd man/tof_annotate_clusters.Rd man/tof_apply_classifier.Rd man/tof_assess_channels.Rd man/tof_assess_clusters_distance.Rd man/tof_assess_clusters_entropy.Rd man/tof_assess_clusters_knn.Rd man/tof_assess_flow_rate.Rd man/tof_assess_flow_rate_tibble.Rd man/tof_assess_model.Rd man/tof_assess_model_new_data.Rd man/tof_assess_model_tuning.Rd man/tof_batch_correct.Rd man/tof_batch_correct_quantile.Rd man/tof_batch_correct_quantile_tibble.Rd man/tof_batch_correct_rescale.Rd man/tof_build_classifier.Rd man/tof_calculate_flow_rate.Rd man/tof_check_model_args.Rd man/tof_classify_cells.Rd man/tof_clean_metric_names.Rd man/tof_cluster.Rd man/tof_cluster_ddpr.Rd man/tof_cluster_flowsom.Rd man/tof_cluster_grouped.Rd man/tof_cluster_kmeans.Rd man/tof_cluster_phenograph.Rd man/tof_cluster_tibble.Rd man/tof_compute_km_curve.Rd man/tof_cosine_dist.Rd man/tof_create_grid.Rd man/tof_create_recipe.Rd man/tof_downsample.Rd man/tof_downsample_constant.Rd man/tof_downsample_density.Rd man/tof_downsample_prop.Rd man/tof_estimate_density.Rd man/tof_extract_central_tendency.Rd man/tof_extract_emd.Rd man/tof_extract_features.Rd man/tof_extract_jsd.Rd man/tof_extract_proportion.Rd man/tof_extract_threshold.Rd man/tof_find_best.Rd man/tof_find_cv_predictions.Rd man/tof_find_emd.Rd man/tof_find_jsd.Rd man/tof_find_knn.Rd man/tof_find_log_rank_threshold.Rd man/tof_find_panel_info.Rd man/tof_fit_split.Rd man/tof_generate_palette.Rd man/tof_get_model_mixture.Rd man/tof_get_model_outcomes.Rd man/tof_get_model_penalty.Rd man/tof_get_model_training_data.Rd man/tof_get_model_type.Rd man/tof_get_model_x.Rd man/tof_get_model_y.Rd man/tof_get_panel.Rd man/tof_is_numeric.Rd man/tof_knn_density.Rd man/tof_log_rank_test.Rd man/tof_make_knn_graph.Rd man/tof_make_roc_curve.Rd man/tof_metacluster.Rd man/tof_metacluster_consensus.Rd man/tof_metacluster_flowsom.Rd man/tof_metacluster_hierarchical.Rd man/tof_metacluster_kmeans.Rd man/tof_metacluster_phenograph.Rd man/tof_plot_cells_density.Rd man/tof_plot_cells_embedding.Rd man/tof_plot_cells_layout.Rd man/tof_plot_cells_scatter.Rd man/tof_plot_clusters_heatmap.Rd man/tof_plot_clusters_mst.Rd man/tof_plot_clusters_volcano.Rd man/tof_plot_heatmap.Rd man/tof_plot_model.Rd man/tof_plot_model_linear.Rd man/tof_plot_model_logistic.Rd man/tof_plot_model_multinomial.Rd man/tof_plot_model_survival.Rd man/tof_plot_sample_features.Rd man/tof_plot_sample_heatmap.Rd man/tof_postprocess.Rd man/tof_predict.Rd man/tof_prep_recipe.Rd man/tof_preprocess.Rd man/tof_read_csv.Rd man/tof_read_data.Rd man/tof_read_fcs.Rd man/tof_read_file.Rd man/tof_reduce_dimensions.Rd man/tof_reduce_pca.Rd man/tof_reduce_tsne.Rd man/tof_reduce_umap.Rd man/tof_set_panel.Rd man/tof_spade_density.Rd man/tof_split_data.Rd man/tof_split_tidytof_reduced_dimensions.Rd man/tof_train_model.Rd man/tof_transform.Rd man/tof_tune_glmnet.Rd man/tof_upsample.Rd man/tof_upsample_distance.Rd man/tof_upsample_neighbor.Rd man/tof_write_csv.Rd man/tof_write_data.Rd man/tof_write_fcs.Rd man/where.Rd tests/spelling.R tests/testthat.R tests/testthat/test-batch_correction.R tests/testthat/test-clustering.R tests/testthat/test-developmental_classifier.R tests/testthat/test-differential_discovery.R tests/testthat/test-dimensionality_reduction.R tests/testthat/test-downsampling.R tests/testthat/test-feature_extraction.R tests/testthat/test-io.R tests/testthat/test-metaclustering.R tests/testthat/test-patient-level_modeling.R tests/testthat/test-preprocessing.R tests/testthat/test-quality_control.R tests/testthat/test-tof_tbl.R tests/testthat/test-upsample.R tests/testthat/test-utils.R tests/testthat/test-visualization.R vignettes/clustering.Rmd vignettes/contributing-to-tidytof.Rmd vignettes/differential-discovery-analysis.Rmd vignettes/dimensionality-reduction.Rmd vignettes/downsampling.Rmd vignettes/feature-extraction.Rmd vignettes/modeling.Rmd vignettes/preprocessing.Rmd vignettes/quality-control.Rmd vignettes/reading-and-writing-data.Rmd vignettes/tidytof.Rmd