Man pages for prybakowska/CytoQP
Cytometry data quality control and cleaninig
| aggregate_files | Deconvolute and aggregate debarcoded files |
| aof_scoring | Calculates AOF scores and scaled AOF scores |
| baseline_file | Creates baseline file for bead normalization |
| bead_normalize | Bead-based normalization |
| clean_files | Clean flow rate and signal |
| debarcode_files | Debarcodes files |
| dot-flow_rate_bin_adapted | flow_rate_bin_adapted |
| dot-gate_out_beads | gate_out_beads |
| dot-make_breaks | Calculates breaks for flow frame splitting |
| dot-plot_flowrate | Plots flow rate |
| dot-remove_mad_outliers | remove_mad_outliers |
| dot-split_flowFrames | Calculates beginning and end of each flow frame. Code from... |
| extract_pctgs_msi_per_flowsom | #' Extracts percentages and MSI for cell populations #' #'... |
| file_outlier_detecion | Detects outliers based on sample quality scores |
| file_quality_check | Check the quality of acquired files |
| find_mass_ch | Finds all the mass/fluorochrome channels for the flow frame |
| fsom_aof | Prepares FlowSOM |
| gate_intact_cells | Gate intact cells |
| gate_live_cells | Gate live cells |
| gate_singlet_cells | Gate singlet cells |
| grid_arrange_common_legend | Plot listed plots with one common legend |
| meta_data | Meta data containing information about sample aquisition,... |
| normalize_REF | Normalize the data |
| plot_2D_scatter_plots | Plot 2D scatter plots |
| plot_batch | Visualize batch using umap dimensional reduction |
| plot_batch_using_freq_msi | Plot the distribution of the features across batches in two... |
| plot_marker_quantiles | Plots quantiles for the markers |
| prepare_data_for_plotting | Prepares data for plotting cell frequency and MSI |
| scaled_aof_score | Calculates scaled aof scores and sample quality scores |
| split_big_flowFrames | Split big flow frames into smaller fcs files |
| test_match_order | Tests the order of the files |
| train_REF_model | Normalize using reference sample |
