Man pages for DillonHammill/CytoExploreR
Interactive Analysis of Cytometry Data
| cyto_apply | Apply a function over cytometry objects |
| cyto_barcode | Barcode each file in a flowSet with a sample ID |
| cyto_beads_sample | Sample GatingSet to bead count |
| cyto_calibrate | Calibrate channel ranges for cyto_plot |
| cyto_calibrate_reset | Remove current calibration settings |
| cyto_channel_match | Table Editor for Channel Match File Construction |
| cyto_channels | Extract channel names |
| cyto_channel_select | Select Fluorescent Channel for Compensation Controls |
| cyto_channels_extract | Extract channels associated with certain markers |
| cyto_channels_restrict | Restrict the channels of a cytometry object |
| cyto_check | Check a flowFrame, flowSet, GatingHierarchy or GatingSet has... |
| cyto_clean | Apply flowAI anomaly detection to clean cytometry data |
| cyto_compensate | Apply fluorescence compensation to samples |
| cyto_convert | Convert between cytometry objects |
| cyto_copy | Copy a cytoset, cytoframe or GatingSet |
| cyto_details | Extract experiment details |
| cyto_details_edit | Interactively edit cyto_details for a flowSet or GatingSet |
| cyto_details_save | Save experiment details to csv file |
| cyto_empty | Construct an empty flowFrame |
| cyto_export | Export cytometry data for use in flowJo or Cytobank |
| cyto_extract | Extract a valid flowFrame or flowSet |
| cyto_filter | Filter samples based on experiment variables |
| cyto_fluor_channels | Extract Fluorescent Channels |
| cyto_gate_bool | Add boolean gate to GatingSet and gatingTemplate |
| cyto_gate_convert | Convert Between 1D and 2D Gate Objects |
| cyto_gate_copy | Copy gates to other nodes in GatingSet and update... |
| cyto_gate_draw | Interactively draw and construct gate objects |
| cyto_gate_edit | Edit Existing Gate(s). |
| cyto_gate_extract | Extract Saved Gate(s) from gatingTemplate. |
| cyto_gate_remove | Remove Gate(s) and Edit gatingTemplate csv File |
| cyto_gate_rename | Rename Gates |
| cyto_gate_transform | Transform gates objects |
| cyto_gate_type | Get Gate Type from Saved Gate. |
| cyto_gatingTemplate_active | Active gatingTemplate |
| cyto_gatingTemplate_apply | Apply gates saved in gatingTemplate to a GatingHierarchy or... |
| cyto_gatingTemplate_create | Create an empty gatingTemplate csv file |
| cyto_gatingTemplate_edit | Interactively Edit a gatingTemplate |
| cyto_gatingTemplate_generate | Generate a CytoExploreR gatingTemplate for a GatingHierarchy... |
| cyto_gatingTemplate_read | Read in a gatingTemplate object or gatingTemplate csv file |
| cyto_gatingTemplate_select | Select a gatingTemplate for downstream analyses |
| cyto_gatingTemplate_update | Convert CytoRSuite gatingTemplate to be compatible with... |
| cyto_gatingTemplate_write | Write gatingTemplate to csv file |
| cyto_group_by | Group a flowSet or GatingSet by experiment variables |
| cyto_load | Load .fcs files into ncdfFlowSet |
| cyto_map | Create dimension-reduced maps of cytometry data |
| cyto_markers | Extract marker names |
| cyto_markers_edit | Assign marker names to flowFrame or flowSet |
| cyto_markers_extract | Extract marker names for certain channels |
| cyto_merge_by | Merge a flowSet by experiment variables |
| cyto_names | Extract sample names |
| cyto_names_parse | Parse file names into experiment details |
| cyto_names-set | Replacement method for cyto_names |
| cyto_nodes | Extract Names of Gated Populations in GatingHierarchy or... |
| cyto_nodes_ancestor | Get name of most recent common ancestor shared by nodes |
| cyto_nodes_convert | Convert to unique node paths |
| cyto_plot | cyto_plot |
| cyto_plot_compensation | Visualise Compensation of Fluorescent Spillover in All... |
| cyto_plot_complete | Indicate Completion of Custom cyto_plot Layout for Saving |
| cyto_plot_contour | Add contour lines to cyto_plot |
| cyto_plot_custom | Create custom cyto_plot |
| cyto_plot_density | Add density distributions to empty plots |
| cyto_plot_empty | Create an empty cyto_plot |
| cyto_plot_explore | Explore Cytometry Data in Bivariate Plots |
| cyto_plot_gate | Plot Gate Objects onto an Existing cyto_plot |
| cyto_plot_gating_scheme | Plot Cytometry Gating Strategies |
| cyto_plot_gating_tree | Plot Gating Trees |
| cyto_plot_label | Add labels to cyto_plot |
| cyto_plot_labeller | Add labels to existing cyto_plot |
| cyto_plot_layout | Set Panel Layout for cyto_plot |
| cyto_plot_new | Open new graphics device for cyto_plot |
| cyto_plot_point | Add points and contour lines to empty cyto_plot |
| cyto_plot_profile | Plot expression profile in all channels |
| cyto_plot_record | Record an existing cyto_plot |
| cyto_plot_reset | Reset all cyto_plot related settings |
| cyto_plot_save | Save High Resolution cyto_plot Images |
| cyto_plot_save_reset | Revert unwanted cyto_plot_save call |
| cyto_plot_theme | Create custom themes for cyto_plot |
| cyto_plot_theme_args | Get supported cyto_plot_theme arguments |
| cyto_plot_theme_reset | Reset cyto_plot_theme to default settings |
| cyto_sample | Sample a flowFrame or flowSet |
| cyto_save | Write samples to FCS files in new folder or save GatingSet |
| cyto_select | Select samples based on experiment variables |
| cyto_setup | Load.fcs files into GatingSet and annotate with experiment... |
| cyto_spillover_compute | Compute Spillover Matrix |
| cyto_spillover_edit | Interactively Edit Spillover Matrices in Real-Time |
| cyto_spillover_extract | Extract spillover matrix from cytometry object |
| cyto_spillover_spread_compute | Compute Spillover Spreading Matrix |
| cyto_split | Split samples merged with cyto_merge |
| cyto_stats_compute | Compute, export and save statistics |
| cyto_transform | Apply Transformations to Cytometry Data |
| cyto_transformer_arcsinh | Definition(s) of arcsinh transformation(s) |
| cyto_transformer_biex | Definition(s) of biexponential transformation(s) |
| cyto_transformer_combine | Combine cyto_transformer definitions |
| cyto_transformer_extract | Extract transformers from a GatingHierarchy or GatingSet |
| cyto_transformer_log | Definition(s) of Log Transformation(s) |
| cyto_transformer_logicle | Definition(s) of logicle transformation(s) |
| cyto_transform_extract | Extract Transformations from TransformerList |
| data_editor | Interactive data editor |
| fftRtsne | FIt-SNE Based on Kluger Lab FIt-SNE |
| file_wd_check | Check if a file exists in the current working directory |
