as_SingleCellExperiment
                        Coerce an object into a 'SingleCellExperiment'
as_flowFrame            Coerce an object into a 'flowFrame'
as_flowSet              Coerce an object into a 'flowSet'
as_seurat               Coerce an object into a 'SeuratObject'
as_tof_tbl              Coerce flowFrames or flowSets into tof_tbl's.
as_tof_tbl.flowSet      Convert an object into a tof_tbl
cosine_similarity       Find the cosine similarity between two vectors
ddpr_data               CyTOF data from two samples: 5,000 B-cell
                        lineage cells from a healthy patient and 5,000
                        B-cell lineage cells from a B-cell precursor
                        Acute Lymphoblastic Leukemia (BCP-ALL) patient.
ddpr_metadata           Clinical metadata for each patient sample in
                        Good & Sarno et al. (2018).
dot                     Find the dot product between two vectors.
get_extension           Find the extension for a file
l2_normalize            L2 normalize an input vector x to a length of 1
magnitude               Find the magnitude of a vector.
make_flowcore_annotated_data_frame
                        Make the AnnotatedDataFrame needed for the
                        flowFrame class
metal_masterlist        A character vector of metal name patterns
                        supported by tidytof.
new_tof_model           Constructor for a tof_model.
new_tof_tibble          Constructor for a tof_tibble.
phenograph_data         CyTOF data from 6,000 healthy immune cells from
                        a single patient.
rev_asinh               Reverses arcsinh transformation with cofactor
                        'scale_factor' and a shift of 'shift_factor'.
tidytof_example_data    Get paths to tidytof example data
tof_analyze_abundance   Perform Differential Abundance Analysis (DAA)
                        on high-dimensional cytometry data
tof_analyze_abundance_diffcyt
                        Differential Abundance Analysis (DAA) with
                        diffcyt
tof_analyze_abundance_glmm
                        Differential Abundance Analysis (DAA) with
                        generalized linear mixed-models (GLMMs)
tof_analyze_abundance_ttest
                        Differential Abundance Analysis (DAA) with
                        t-tests
tof_analyze_expression
                        Perform Differential Expression Analysis (DEA)
                        on high-dimensional cytometry data
tof_analyze_expression_diffcyt
                        Differential Expression Analysis (DEA) with
                        diffcyt
tof_analyze_expression_lmm
                        Differential Expression Analysis (DEA) with
                        linear mixed-models (LMMs)
tof_analyze_expression_ttest
                        Differential Expression Analysis (DEA) with
                        t-tests
tof_annotate_clusters   Manually annotate tidytof-computed clusters
                        using user-specified labels
tof_apply_classifier    Perform developmental clustering on CyTOF data
                        using a pre-fit classifier
tof_assess_channels     Detect low-expression (i.e. potentially failed)
                        channels in high-dimensional cytometry data
tof_assess_clusters_distance
                        Assess a clustering result by calculating the
                        z-score of each cell's mahalanobis distance to
                        its cluster centroid and flagging outliers.
tof_assess_clusters_entropy
                        Assess a clustering result by calculating the
                        shannon entropy of each cell's mahalanobis
                        distance to all cluster centroids and flagging
                        outliers.
tof_assess_clusters_knn
                        Assess a clustering result by calculating a
                        cell's cluster assignment to that of its K
                        nearest neighbors.
tof_assess_flow_rate    Detect flow rate abnormalities in
                        high-dimensional cytometry data
tof_assess_flow_rate_tibble
                        Detect flow rate abnormalities in
                        high-dimensional cytometry data (stored in a
                        single data.frame)
tof_assess_model        Assess a trained elastic net model
tof_assess_model_new_data
                        Compute a trained elastic net model's
                        performance metrics using new_data.
tof_assess_model_tuning
                        Access a trained elastic net model's
                        performance metrics using its tuning data.
tof_batch_correct       Perform groupwise linear rescaling of
                        high-dimensional cytometry measurements
tof_batch_correct_quantile
                        Batch-correct a tibble of high-dimensional
                        cytometry data using quantile normalization.
tof_batch_correct_quantile_tibble
                        Batch-correct a tibble of high-dimensional
                        cytometry data using quantile normalization.
tof_batch_correct_rescale
                        Perform groupwise linear rescaling of
                        high-dimensional cytometry measurements
tof_build_classifier    Calculate centroids and covariance matrices for
                        each cell subpopulation in healthy CyTOF data.
tof_calculate_flow_rate
                        Calculate the relative flow rates of different
                        timepoints throughout a flow or mass cytometry
                        run.
tof_check_model_args    Check argument specifications for a glmnet
                        model.
tof_classify_cells      Classify each cell (i.e. each row) in a matrix
                        of cancer cells into its most similar healthy
                        developmental subpopulation.
tof_clean_metric_names
                        Rename glmnet's default model evaluation
                        metrics to make them more interpretable
tof_cluster             Cluster high-dimensional cytometry data.
tof_cluster_ddpr        Perform developmental clustering on
                        high-dimensional cytometry data.
tof_cluster_flowsom     Perform FlowSOM clustering on high-dimensional
                        cytometry data
tof_cluster_grouped     Cluster (grouped) high-dimensional cytometry
                        data.
tof_cluster_kmeans      Perform k-means clustering on high-dimensional
                        cytometry data.
tof_cluster_phenograph
                        Perform PhenoGraph clustering on
                        high-dimensional cytometry data.
tof_cluster_tibble      Cluster (ungrouped) high-dimensional cytometry
                        data.
tof_compute_km_curve    Compute a Kaplan-Meier curve from sample-level
                        survival data
tof_cosine_dist         A function for finding the cosine distance
                        between each of the rows of a numeric matrix
                        and a numeric vector.
tof_create_grid         Create an elastic net hyperparameter search
                        grid of a specified size
tof_create_recipe       Create a recipe for preprocessing sample-level
                        cytometry data for an elastic net model
tof_downsample          Downsample high-dimensional cytometry data.
tof_downsample_constant
                        Downsample high-dimensional cytometry data by
                        randomly selecting a constant number of cells
                        per group.
tof_downsample_density
                        Downsample high-dimensional cytometry data by
                        randomly selecting a proportion of the cells in
                        each group.
tof_downsample_prop     Downsample high-dimensional cytometry data by
                        randomly selecting a proportion of the cells in
                        each group.
tof_estimate_density    Estimate the local densities for all cells in a
                        high-dimensional cytometry dataset.
tof_extract_central_tendency
                        Extract the central tendencies of CyTOF markers
                        in each cluster in a 'tof_tibble'.
tof_extract_emd         Extract aggregated features from CyTOF data
                        using earth-mover's distance (EMD)
tof_extract_features    Extract aggregated, sample-level features from
                        CyTOF data.
tof_extract_jsd         Extract aggregated features from CyTOF data
                        using the Jensen-Shannon Distance (JSD)
tof_extract_proportion
                        Extract the proportion of cells in each cluster
                        in a 'tof_tibble'.
tof_extract_threshold   Extract aggregated features from CyTOF data
                        using a binary threshold
tof_find_best           Find the optimal hyperparameters for an elastic
                        net model from candidate performance metrics
tof_find_cv_predictions
                        Calculate and store the predicted outcomes for
                        each validation set observation during model
                        tuning
tof_find_emd            Find the earth-mover's distance between two
                        numeric vectors
tof_find_jsd            Find the Jensen-Shannon Divergence (JSD)
                        between two numeric vectors
tof_find_knn            Find the k-nearest neighbors of each cell in a
                        high-dimensional cytometry dataset.
tof_find_log_rank_threshold
                        Compute the log-rank test p-value for the
                        difference between the two survival curves
                        obtained by splitting a dataset into a "low"
                        and "high" risk group using all possible
                        relative-risk thresholds.
tof_find_panel_info     Use tidytof's opinionated heuristic for
                        extracted a high-dimensional cytometry panel's
                        metal-antigen pairs from a flowFrame (read from
                        a .fcs file.)
tof_fit_split           Fit a glmnet model and calculate performance
                        metrics using a single rsplit object
tof_generate_palette    Generate a color palette using tidytof.
tof_get_model_mixture   Get a 'tof_model''s optimal mixture (alpha)
                        value
tof_get_model_outcomes
                        Get a 'tof_model''s outcome variable name(s)
tof_get_model_penalty   Get a 'tof_model''s optimal penalty (lambda)
                        value
tof_get_model_training_data
                        Get a 'tof_model''s training data
tof_get_model_type      Get a 'tof_model''s model type
tof_get_model_x         Get a 'tof_model''s processed predictor matrix
                        (for glmnet)
tof_get_model_y         Get a 'tof_model''s processed outcome variable
                        matrix (for glmnet)
tof_get_panel           Get panel information from a tof_tibble
tof_is_numeric          Find if a vector is numeric
tof_knn_density         Estimate cells' local densities using
                        K-nearest-neighbor density estimation
tof_log_rank_test       Compute the log-rank test p-value for the
                        difference between the two survival curves
                        obtained by splitting a dataset into a "low"
                        and "high" risk group using a given
                        relative-risk threshold.
tof_make_knn_graph      Title
tof_make_roc_curve      Compute a receiver-operating curve (ROC) for a
                        two-class or multiclass dataset
tof_metacluster         Metacluster clustered CyTOF data.
tof_metacluster_consensus
                        Metacluster clustered CyTOF data using
                        consensus clustering
tof_metacluster_flowsom
                        Metacluster clustered CyTOF data using
                        FlowSOM's built-in metaclustering algorithm
tof_metacluster_hierarchical
                        Metacluster clustered CyTOF data using
                        hierarchical agglomerative clustering
tof_metacluster_kmeans
                        Metacluster clustered CyTOF data using k-means
                        clustering
tof_metacluster_phenograph
                        Metacluster clustered CyTOF data using
                        PhenoGraph clustering
tof_plot_cells_density
                        Plot marker expression density plots
tof_plot_cells_embedding
                        Plot scatterplots of single-cell data using
                        low-dimensional feature embeddings
tof_plot_cells_layout   Plot force-directed layouts of single-cell data
tof_plot_cells_scatter
                        Plot scatterplots of single-cell data.
tof_plot_clusters_heatmap
                        Make a heatmap summarizing cluster marker
                        expression patterns in CyTOF data
tof_plot_clusters_mst   Visualize clusters in CyTOF data using a
                        minimum spanning tree (MST).
tof_plot_clusters_volcano
                        Create a volcano plot from differential
                        expression analysis results
tof_plot_heatmap        Make a heatmap summarizing group marker
                        expression patterns in high-dimensional
                        cytometry data
tof_plot_model          Plot the results of a glmnet model fit on
                        sample-level data.
tof_plot_model_linear   Plot the results of a linear glmnet model fit
                        on sample-level data.
tof_plot_model_logistic
                        Plot the results of a two-class glmnet model
                        fit on sample-level data.
tof_plot_model_multinomial
                        Plot the results of a multiclass glmnet model
                        fit on sample-level data.
tof_plot_model_survival
                        Plot the results of a survival glmnet model fit
                        on sample-level data.
tof_plot_sample_features
                        Make a heatmap summarizing sample marker
                        expression patterns in CyTOF data
tof_plot_sample_heatmap
                        Make a heatmap summarizing sample marker
                        expression patterns in CyTOF data
tof_postprocess         Post-process transformed CyTOF data.
tof_predict             Use a trained elastic net model to predict
                        fitted values from new data
tof_prep_recipe         Train a recipe or list of recipes for
                        preprocessing sample-level cytometry data
tof_preprocess          Preprocess raw high-dimensional cytometry data.
tof_read_csv            Read high-dimensional cytometry data from a
                        .csv file into a tidy tibble.
tof_read_data           Read data from an .fcs/.csv file or a directory
                        of .fcs/.csv files.
tof_read_fcs            Read high-dimensional cytometry data from an
                        .fcs file into a tidy tibble.
tof_read_file           Read high-dimensional cytometry data from a
                        single .fcs or .csv file into a tidy tibble.
tof_reduce_dimensions   Apply dimensionality reduction to a single-cell
                        dataset.
tof_reduce_pca          Perform principal component analysis on
                        single-cell data
tof_reduce_tsne         Perform t-distributed stochastic neighborhood
                        embedding on single-cell data
tof_reduce_umap         Apply uniform manifold approximation and
                        projection (UMAP) to single-cell data
tof_set_panel           Set panel information from a tof_tibble
tof_spade_density       Estimate cells' local densities as done in
                        Spanning-tree Progression Analysis of
                        Density-normalized Events (SPADE)
tof_split_data          Split high-dimensional cytometry data into a
                        training and test set
tof_split_tidytof_reduced_dimensions
                        Split the dimensionality reduction data that
                        tidytof combines during 'SingleCellExperiment'
                        conversion
tof_train_model         Train an elastic net model to predict
                        sample-level phenomena using high-dimensional
                        cytometry data.
tof_transform           Transform raw high-dimensional cytometry data.
tof_tune_glmnet         Tune an elastic net model's hyperparameters
                        over multiple resamples
tof_upsample            Upsample cells into the closest cluster in a
                        reference dataset
tof_upsample_distance   Upsample cells into the closest cluster in a
                        reference dataset
tof_upsample_neighbor   Upsample cells into the cluster of their
                        nearest neighbor a reference dataset
tof_write_csv           Write a series of .csv files from a tof_tbl
tof_write_data          Write high-dimensional cytometry data to a file
                        or to a directory of files
tof_write_fcs           Write a series of .fcs files from a tof_tbl
where                   Select variables with a function
