Man pages for biosurf/cyCombine
Robust integration of single-cell cytometry datasets within and across technologies

batch_correctRun batch correction on data
compile_fcsCompile all .fcs files in a directory to a flowset
compute_emdCompute EMD
compute_madCompute MAD
convert_flowsetConvert a flowSet into a tibble
correct_dataCorrect data using ComBat
correct_data_altAlternate correction
create_somCreate Self-Organizing Map
detect_batch_effectFull function for detection of batch effects using cluster...
detect_batch_effect_expressQuicker function for detection of batch effects
df2SCEExporting a dataframe to SingleCellObject
evaluate_emdEvaluate Earth Mover's Distance
evaluate_madEvaluate MAD
get_markersGet markers from a dataframe
impute_across_panelsImpute non-overlapping channels for whole data sets
non_markersColumn names that are not cytometry markers
normalizeBatch-wise normalization of data
pipePipe operator
plot_densityDensity ridges for two sets
plot_dimredDimensionality reduction plot
plot_dimred_fullDimensionality reduction plots - colored with labels, batches...
plot_save_fourSave four plots aligned with cowplot
plot_save_twoSave two plots aligned with cowplot
plot_umap_labelsDimensionality reduction plots for a two-batch dataset before...
prepare_dataPrepare a directory of .fcs files
quantile_normBatch-wise quantile normalization per marker
randomize_matrixRandomize a matrix of values
run_analysisRun analysis of a batch correction
salvage_problematicSalvaging problematic channels - one at a time
sce2FCSConvert SingelCellExperiment into flowSet and store as FCS...
transform_asinhTransform data using asinh
biosurf/cyCombine documentation built on May 23, 2024, 4:07 a.m.