batch_correct | Run batch correction on data |
compile_fcs | Compile all .fcs files in a directory to a flowset |
compute_emd | Compute EMD |
compute_mad | Compute MAD |
convert_flowset | Convert a flowSet into a tibble |
correct_data | Correct data using ComBat |
correct_data_alt | Alternate correction |
create_som | Create Self-Organizing Map |
detect_batch_effect | Full function for detection of batch effects using cluster... |
detect_batch_effect_express | Quicker function for detection of batch effects |
df2SCE | Exporting a dataframe to SingleCellObject |
evaluate_emd | Evaluate Earth Mover's Distance |
evaluate_mad | Evaluate MAD |
get_markers | Get markers from a dataframe |
impute_across_panels | Impute non-overlapping channels for whole data sets |
non_markers | Column names that are not cytometry markers |
normalize | Batch-wise normalization of data |
pipe | Pipe operator |
plot_density | Density ridges for two sets |
plot_dimred | Dimensionality reduction plot |
plot_dimred_full | Dimensionality reduction plots - colored with labels, batches... |
plot_save_four | Save four plots aligned with cowplot |
plot_save_two | Save two plots aligned with cowplot |
plot_umap_labels | Dimensionality reduction plots for a two-batch dataset before... |
prepare_data | Prepare a directory of .fcs files |
quantile_norm | Batch-wise quantile normalization per marker |
randomize_matrix | Randomize a matrix of values |
run_analysis | Run analysis of a batch correction |
salvage_problematic | Salvaging problematic channels - one at a time |
sce2FCS | Convert SingelCellExperiment into flowSet and store as FCS... |
transform_asinh | Transform data using asinh |
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