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Data Loading

Functions to load data to a condor object.

prep_fcd()
prep_fcd
prep_fjw()
Read FlowJo Workspace
transform_data()
transform_data
clr()
crt_transform
read_data()
read_data

Dimensionality Reduction

Dimensionality reduction functions.

runPCA_pseudobulk()
runPCA_pseudobulk
runPCA()
runPCA
runUMAP()
runUMAP
runtSNE()
runtSNE
runDM()
runDM

Clustering

Clustering functions.

runPhenograph()
runPhenograph
runFlowSOM()
runFlowSOM
metaclustering()
metaclustering

Batch Correction

Implementation of Harmony.

harmonize_PCA()
harmonize_PCA
harmonize_intensities()
harmonize_intensities
train_cytonorm()
train_cytonorm
run_cytonorm()
run_cytonorm

Pseudotime

Implementation of slingshot.

runPseudotime()
Function of calculate Pseudotime from HDFC data analysed with cyCONDOR

Classifier and Data Projection

Machine learning classifier and data projection.

train_classifier_model()
Train a machine learning classifier for the clinical classification of HDFC data.
train_transfer_model()
train_transfer_model
predict_classifier()
Predict clinical classification.
predict_labels()
predict_labels
learnUMAP()
learnUMAP
runAstir_cellstates()
runAstir_cellstates
runAstir_celltype()
Run Astir cell type prediction

Data Visualization

Collection of functions to visualize the results.

getTable()
Get summary values
PC_loadings()
PC_loadings
plot_frequency_boxplot()
box plot of cell population frequencies
plot_frequency_barplot()
bar chart of cell population frequencies
plot_counts_barplot()
bar chart of cell population counts
plot_confusion_HM()
plot_confusion_HM
confusionMatrix()
confusionMatrix
plot_marker_density()
density plot of marker expression in cell populations grouped by a meta variable
plot_marker_group_HM()
Heatmap of scaled expression to compare two groups
plot_marker_HM()
Heatmap of scaled expression by cell population
plot_dim_density()
dimensionality reduction plot with density distribution
plot_dim_red()
Dimensionality reduction dotplot
plot_marker_violinplot()
violin plot of marker expression in cell populations
plot_marker_boxplot()
plot box plots of marker median or mean
plot_marker_dotplot()
plot_marker_dotplot
plot_marker_ridgeplot()
ridgeline plot of marker expression in cell populations

Differential Testing

Collection of functions to calculate differential abundance and expression.

frequency_anova_test()
Anova test to compare cell population frequencies of independent samples
frequency_friedman_test()
Friedman Rank Sum test to compare cell population frequencies of paired samples
frequency_kruskal_test()
Kruskal-Wallis test to compare cell population frequencies
frequency_t_test()
t-test to compare cell population frequencies
frequency_wilcox_test()
Wilcoxon test to compare cell population frequencies
prepInputDiffcyt()
Convert a condor object to se object
marker_wilcox_test()
Differential expression testing on cell level

Utilities

Collection of misc functions.

scaleColors()
scaleColors
used_markers()
used_markers
change_param_name()
change_param
check_IDs()
check_IDs
df_frequency()
df_frequency
filter_fcd()
filter_fcd
merge_condor()
merge_condor
subset_fcd()
subset_fcd
subset_fcd_byparam()
subset_fcd_byparam
checkInput()
Helper function within cyCONDOR
measured_markers()
measured_markers