Files in keyes-timothy/tidytof
Analyze High-dimensional Cytometry Data Using Tidy Data Principles
.Rbuildignore
.github/.gitignore
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/issue_template.md
.github/workflows/R-CMD-check.yaml
.github/workflows/check-bioc.yml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
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/sysdata.rda
R/tidytof-package.R
R/tof_tbl.R
R/upsample.R
R/utils.R
R/visualization.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data/ddpr_data.rda
data/ddpr_metadata.rda
data/metal_masterlist.rda
data/phenograph_data.rda
inst/CITATION
inst/WORDLIST
inst/extdata/aml/bm5721_healthy_basal.fcs
inst/extdata/aml/parbiu_dx_basal.fcs
inst/extdata/ddpr/Healthy1_Basal.fcs
inst/extdata/ddpr/UPN1_Basal.fcs
inst/extdata/ddpr_metadata.csv
inst/extdata/mix/H1_PhenoGraph_cluster1.fcs
inst/extdata/mix/bm5721_healthy_basal.fcs
inst/extdata/mix2/H1_PhenoGraph_cluster1.csv
inst/extdata/mix2/H1_PhenoGraph_cluster2.csv
inst/extdata/mix2/bm5721_healthy_basal.fcs
inst/extdata/phenograph/H1_PhenoGraph_cluster1.fcs
inst/extdata/phenograph/H1_PhenoGraph_cluster2.fcs
inst/extdata/phenograph/H1_PhenoGraph_cluster3.fcs
inst/extdata/phenograph_csv/H1_PhenoGraph_cluster1.csv
inst/extdata/phenograph_csv/H1_PhenoGraph_cluster2.csv
inst/extdata/scaffold/Blood_Balb.fcs
inst/extdata/scaffold/BoneMarrow_129.fcs
inst/extdata/scaffold/Colon_129.fcs
inst/extdata/statistical_scaffold/TIN_TU1_B6Antibodies_Day8.fcs
inst/extdata/statistical_scaffold/TIN_TU1_Untreated_Day8.fcs
inst/extdata/surgery/121002hipsurg_102_1h.fcs
inst/extdata/surgery/121002hipsurg_102_1mo.fcs
inst/extdata/surgery/121002hipsurg_102_24h.fcs
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/figures/README-unnamed-chunk-16-1.png
man/figures/README-unnamed-chunk-17-1.png
man/figures/README-unnamed-chunk-18-1.png
man/figures/README-unnamed-chunk-24-1.png
man/figures/README-unnamed-chunk-24-2.png
man/figures/README-unnamed-chunk-25-1.png
man/figures/README-unnamed-chunk-25-2.png
man/figures/README-unnamed-chunk-30-1.png
man/figures/README-unnamed-chunk-31-1.png
man/figures/README-unnamed-chunk-32-1.png
man/figures/README-unnamed-chunk-33-1.png
man/figures/README-unnamed-chunk-52-1.png
man/figures/README-unnamed-chunk-53-1.png
man/figures/README-unnamed-chunk-54-1.png
man/figures/README-unnamed-chunk-55-1.png
man/figures/README-unnamed-chunk-56-1.png
man/figures/README-unnamed-chunk-57-1.png
man/figures/tidytof_logo.png
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
src/.gitignore
src/RcppExports.cpp
src/code.cpp
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/.gitignore
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
