Comprehensive Lipidomics Data Analysis with Interactive Visualization

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Documentation for package ‘LIPIDIFy’ version 0.99.7

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

apply_normalizations	Apply a Sequence of Normalization Methods
classify_lipids	Classify Lipids Based on Their Names
correct_batch_effects	Correct Batch Effects from a Normalised Lipidomics Matrix
create_default_contrasts	Create Default Contrasts
create_enrichment_barplot	Create an Enrichment Barplot
create_enrichment_dotplot	Create an Enrichment Dotplot
create_heatmap_robust	Create a Robust Heatmap of Top Variable Features
create_lipid_expression_barplot	Create a Lipid Expression Barplot Ordered by Group
create_pca_plot_with_ellipses	Create a PCA Plot with Optional Confidence or Visual Ellipses
create_pipeline_plot	Quick QC Plot for a Normalized Data Matrix
create_plsda_plot_with_ellipses	Create a PLS-DA Plot with Optional Ellipses
create_volcano_plot_labeled	Create a Volcano Plot with Optional Classification Colouring
determine_saturation	Determine Fatty-Acid Saturation from a Lipid Name
export_classification	Export Lipid Classification to CSV
fix_sample_alignment	Align Samples Between Data Matrix and Metadata
generate_example_data	Generate Example Dataset
get_imputation_descriptions	Return Human-Readable Descriptions of Imputation Methods
get_imputation_methods	Return Available Imputation Method Names
get_normalization_descriptions	Return Human-Readable Descriptions of Normalization Methods
get_normalization_methods	Return Available Normalization Method Names
impute_missing_values	Impute Missing Values in a Lipidomics Data Matrix
launch_lipidomics_app	Launch the LIPIDIFy Shiny Application
load_custom_classification	Load Custom Lipid Classification from a CSV File
load_custom_enrichment_sets	Load Custom Enrichment Sets from a CSV File
load_lipidomics_data	Load Lipidomics Data
load_lipidomics_data_from_df	Load Lipidomics Data from Data Frame
normalize_log2median	Log2 Median Centering Normalization
normalize_mean	Mean Normalization
normalize_median	Median Normalization
normalize_pqn	PQN Normalization
normalize_quantile	Quantile Normalization
normalize_tic	TIC Normalization
normalize_vsn	VSN (Variance Stabilizing Normalization)
perform_differential_analysis	Perform Differential Analysis
perform_enrichment_analysis	Perform Enrichment Analysis
perform_pca	Perform PCA Analysis
perform_plsda	Perform PLS-DA Analysis
test_saturation_classification	Test Saturation Classification
visualize_raw_data	Visualize Raw Data
visualize_raw_data_improved	Visualize Raw or Normalized Data with Sample/Lipid Toggle