cyCONDOR/_pkgdown.yml at master · lorenzobonaguro/cyCONDOR · GitHub

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url: https://lorenzobonaguro.github.io/cyCONDOR, https://github.com/lorenzobonaguro/cyCONDOR
template:
  bootstrap: 5
  light-switch: true

reference:
- title: Data Loading
  desc: Functions to load data to a condor object.
  contents:
  - prep_fcd
  - prep_fjw
  - transform_data
  - clr
  - read_data

- title: Dimensionality Reduction
  desc: Dimensionality reduction functions.
  contents:
  - runPCA_pseudobulk
  - runPCA
  - runUMAP
  - runtSNE
  - runDM

- title: Clustering
  desc: Clustering functions.
  contents:
  - runPhenograph
  - runFlowSOM
  - metaclustering

- title: Batch Correction
  desc: Implementation of Harmony.
  contents:
  - harmonize_PCA
  - harmonize_intensities
  - train_cytonorm
  - run_cytonorm

- title: Pseudotime
  desc: Implementation of slingshot.
  contents:
  - runPseudotime

- title: Classifier and Data Projection
  desc: Machine learning classifier and data projection.
  contents:
  - train_classifier_model
  - train_transfer_model
  - predict_classifier
  - predict_labels
  - learnUMAP
  - runAstir_cellstates
  - runAstir_celltype

- title: Data Visualization
  desc: Collection of functions to visualize the results.
  contents:
  - getTable
  - PC_loadings
  - plot_frequency_boxplot
  - plot_frequency_barplot
  - plot_counts_barplot
  - plot_confusion_HM
  - confusionMatrix
  - plot_marker_density
  - plot_marker_group_HM
  - plot_marker_HM
  - plot_dim_density
  - plot_dim_red
  - plot_marker_violinplot
  - plot_marker_boxplot
  - plot_marker_dotplot
  - plot_marker_ridgeplot

- title: Differential Testing
  desc: Collection of functions to calculate differential abundance and expression.
  contents:
  - frequency_anova_test
  - frequency_friedman_test
  - frequency_kruskal_test
  - frequency_t_test
  - frequency_wilcox_test
  - prepInputDiffcyt
  - marker_wilcox_test
  - add_diffcyt_statistics

- title: Utilities
  desc:  Collection of misc functions.
  contents:
  - scaleColors
  - used_markers
  - change_param_name
  - check_IDs
  - df_frequency
  - filter_fcd
  - merge_condor
  - subset_fcd
  - subset_fcd_byparam
  - subsample_geosketch
  - checkInput
  - measured_markers
  - create_metaclustering_script
  - condor_session_info
  - corr_plot_comparison
  - write_fcs
  - condor_info
  - export_sce
  - order_param

articles:
- title: Detailed cyCONDOR workflows
  desc: >
    cyCONDOR tutorials
  navbar: ~
  contents:
  - Prepare_data_for_cyCONDOR_analysis
  - How_to_run_cyCONDOR_as_container
  - Data_Loading_and_Transformation
  - Load_a_FlowJo_workspace
  - Dimensionality_Reduction
  - Clustering_and_cell_annotation
  - Batch_correction
  - Data_Visualization
  - Differential_Analysis
  - Pseudotime_analysis
  - Data_Projection
  - Machine_learning_classifier
  - Cell_type_prediction
  - Other_utilities

- title: Other workflows
  desc: >
    Additional analytical workflows
  contents:
  - Workflow_merge_panels