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# Package index

## 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

`add_diffcyt_statistics()`
  Add statistical results from the diffcyt package to the fcd.

## 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

`subsample_geosketch()`
  Subsampling base on geometric sketching

`checkInput()`
  Helper function within cyCONDOR

`measured_markers()`
  measured_markers

`create_metaclustering_script()`
  create_metaclustering_script

`condor_session_info()`
  condor_session_info

`corr_plot_comparison()`
  Sample-wise correlation of cell type proportions to compare manual gating and cyCONDOR.

`write_fcs()`
  Save the results from cyCONDOR as FCS file(s)

`condor_info()`
  condor_info

`export_sce()`
  Export Flow Cytometry Dataset as SCE.

`order_param()`
  order_param