Prerequisites | Workflow basics | {tidytof} verb syntax | Pipelines | Other tips | Where to go next | Session info

Accessing the data for this vignette | Reading Data with tof_read_data | Using tibble methods with {tidytof} tibbles | Writing data from a tof_tbl to disk | Session info

Accessing the data for this vignette | Detect low-expression (i.e. potentially failed) channels with tof_assess_channels() | Identify time periods of abnormally low or high flow rate during data acquisition using tof_assess_flow_rate() | Flag cells that are unusually far from the centroid of a cluster to which they have been assigned with tof_assess_clusters_distance() | Flag cells whose cluster assignment is ambiguous with tof_assess_clusters_entropy() | Simulated data | Real data | Session info

Preprocessing with tof_preprocess | Postprocessing with tof_postprocess | Session info

Downsampling with tof_downsample() | Additional documentation | Session info

Dimensionality reduction with tof_reduce_dimensions(). | Method specifications for tof_reduce_*() functions | Visualization using tof_plot_cells_embedding() | Session info

Clustering with tof_cluster() | Session info

Accessing the data for this vignette | Differential abundance analysis using tof_analyze_abundance() | Differential expression analysis with tof_analyze_expression() | Session info

Accessing the data for this vignette | Calculating cluster proportions using tof_extract_proportion() | Calculating cluster marker expression measures using tof_extract_central_tendency() | Calculating the proportion of cells with marker expression above a threshold using tof_extract_proportion() | Calculating differences in marker distributions using tof_extract_emd() and tof_extract_jsd() | Putting it all together with tof_extract_features() | Session info

Accessing the data for this vignette | Building a classifier using elastic net-regularized logistic regression | Building a survival model using elastic net-regularized cox regression | Session info

General Guidelines | Code style | Testing | How to contribute | General principles | Contributing a new method to an existing {tidytof} verb | Creating a new {tidytof} verb | A note about modeling functions | Contact us | Session info

Basics | Installing tidyFlowCore | Preliminaries | Asking for help | Citing tidyFlowCore | tidyFlowCore quick start | Load required packages | Read data | Data transformation | Cell type counting | Nesting and unnesting | Plotting | Reproducibility | Bibliography