Function reference
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prep_fcd()
- prep_fcd
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prep_fjw()
- Read FlowJo Workspace
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transform_data()
- transform_data
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clr()
- crt_transform
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read_data()
- read_data
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runPCA_pseudobulk()
- runPCA_pseudobulk
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runPCA()
- runPCA
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runUMAP()
- runUMAP
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runtSNE()
- runtSNE
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runDM()
- runDM
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harmonize_PCA()
- harmonize_PCA
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harmonize_intensities()
- harmonize_intensities
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train_cytonorm()
- train_cytonorm
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run_cytonorm()
- run_cytonorm
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runPseudotime()
- Function of calculate Pseudotime from HDFC data analysed with cyCONDOR
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train_classifier_model()
- Train a machine learning classifier for the clinical classification of HDFC data.
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train_transfer_model()
- train_transfer_model
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predict_classifier()
- Predict clinical classification.
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predict_labels()
- predict_labels
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learnUMAP()
- learnUMAP
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runAstir_cellstates()
- runAstir_cellstates
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runAstir_celltype()
- Run Astir cell type prediction
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getTable()
- Get summary values
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PC_loadings()
- PC_loadings
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plot_frequency_boxplot()
- box plot of cell population frequencies
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plot_frequency_barplot()
- bar chart of cell population frequencies
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plot_counts_barplot()
- bar chart of cell population counts
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plot_confusion_HM()
- plot_confusion_HM
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confusionMatrix()
- confusionMatrix
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plot_marker_density()
- density plot of marker expression in cell populations grouped by a meta variable
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plot_marker_group_HM()
- Heatmap of scaled expression to compare two groups
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plot_marker_HM()
- Heatmap of scaled expression by cell population
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plot_dim_density()
- dimensionality reduction plot with density distribution
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plot_dim_red()
- Dimensionality reduction dotplot
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plot_marker_violinplot()
- violin plot of marker expression in cell populations
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plot_marker_boxplot()
- plot box plots of marker median or mean
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plot_marker_dotplot()
- plot_marker_dotplot
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plot_marker_ridgeplot()
- ridgeline plot of marker expression in cell populations
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frequency_anova_test()
- Anova test to compare cell population frequencies of independent samples
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frequency_friedman_test()
- Friedman Rank Sum test to compare cell population frequencies of paired samples
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frequency_kruskal_test()
- Kruskal-Wallis test to compare cell population frequencies
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frequency_t_test()
- t-test to compare cell population frequencies
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frequency_wilcox_test()
- Wilcoxon test to compare cell population frequencies
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prepInputDiffcyt()
- Convert a condor object to se object
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marker_wilcox_test()
- Differential expression testing on cell level
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scaleColors()
- scaleColors
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used_markers()
- used_markers
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change_param_name()
- change_param
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check_IDs()
- check_IDs
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df_frequency()
- df_frequency
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filter_fcd()
- filter_fcd
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merge_condor()
- merge_condor
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subset_fcd()
- subset_fcd
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subset_fcd_byparam()
- subset_fcd_byparam
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checkInput()
- Helper function within cyCONDOR
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measured_markers()
- measured_markers