Package: LIPIDIFy 0.99.0

Fayrouz Hammal

LIPIDIFy: Comprehensive Lipidomics Data Analysis with Interactive Visualization

Provides a comprehensive toolkit for end-to-end lipidomics data analysis, including missing value imputation, batch effect correction, normalization, differential abundance analysis using limma and edgeR, gene set enrichment analysis, and extensive visualization capabilities. Lipid names are automatically classified by class, subclass, and fatty-acid saturation. Features both an interactive Shiny interface for bench biologists and fully scriptable R functions for bioinformaticians. Supports flexible custom lipid classification schemes and user-defined enrichment sets.

Authors:Fayrouz Hammal [aut, cre]

LIPIDIFy_0.99.0.tar.gz
LIPIDIFy_0.99.0.zip(r-4.7)LIPIDIFy_0.99.0.zip(r-4.6)LIPIDIFy_0.99.0.zip(r-4.5)
LIPIDIFy_0.99.0.tgz(r-4.6-any)LIPIDIFy_0.99.0.tgz(r-4.5-any)
LIPIDIFy_0.99.0.tar.gz(r-4.7-any)LIPIDIFy_0.99.0.tar.gz(r-4.6-any)
LIPIDIFy_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
LIPIDIFy/json (API)
NEWS

# Install 'LIPIDIFy' in R:
install.packages('LIPIDIFy', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fayrouzhammal/lipidify/issues

On CRAN:

Conda:

lipidomicsmassspectrometrynormalizationpreprocessingdifferentialexpressiongenesetenrichmentvisualizationshinyappsmultiplecomparisonbatcheffectqualitycontroldataimport

3.70 score 43 exports 140 dependencies

Last updated from:9d5392819a. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING194
linux-devel-x86_64WARNING212
source / vignettesOK271
linux-release-x86_64WARNING253
macos-release-arm64WARNING98
macos-oldrel-arm64WARNING113
windows-develWARNING188
windows-releaseWARNING191
windows-oldrelWARNING158
wasm-releaseOK174

Exports:apply_normalizationsclassify_lipidscorrect_batch_effectscreate_default_contrastscreate_enrichment_barplotcreate_enrichment_dotplotcreate_heatmap_robustcreate_lipid_expression_barplotcreate_pca_plot_with_ellipsescreate_pipeline_plotcreate_plsda_plot_with_ellipsescreate_volcano_plot_labeleddetermine_saturationexample_lipidomics_dataexport_classificationfix_sample_alignmentgenerate_example_dataget_imputation_descriptionsget_imputation_methodsget_lipid_classificationget_normalization_descriptionsget_normalization_methodsimpute_missing_valueslaunch_lipidomics_appload_custom_classificationload_custom_enrichment_setsload_lipidomics_dataload_lipidomics_data_from_dfnormalize_lipidomics_datanormalize_log2mediannormalize_meannormalize_mediannormalize_pqnnormalize_quantilenormalize_ticnormalize_vsnperform_differential_analysisperform_enrichment_analysisperform_pcaperform_plsdatest_saturation_classificationvisualize_raw_datavisualize_raw_data_improved

Dependencies:abindaskpassbackportsbase64encBHBiocParallelbootbroombslibcachemcarcarDatacliclustercodetoolscolorspacecommonmarkcowplotcpp11crosstalkcurldata.tableDerivdigestdoBydplyrDTedgeRellipseemmeansestimabilityevaluateFactoMineRfarverfastmapfastmatchfgseaflashClustfontawesomeforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsggplot2ggrepelgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4lmtestlocfitmagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivopensslopenxlsxotelpbkrtestpheatmappillarpkgconfigplotlyplspromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownS7sassscalesscatterplot3dshinyshinydashboardsnowsourcetoolsSparseMstatmodstringistringrsurvivalsystibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunxtableyamlzipzoo

LIPIDIFy: A Complete Lipidomics Analysis Workflow

Fayrouz Hammal

Rendered fromlipidomics-workflow.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-05-04
Started: 2026-04-30

LIPIDIFy: Comprehensive Lipidomics Data Analysis

Your Name

Rendered fromlipidomics-analyser-guide.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-05-04
Started: 2026-01-19

Readme and manuals

Help Manual

Help pageTopics
Apply a Sequence of Normalization Methodsapply_normalizations
Build the Rmd Content for the Analysis Reportbuild_report_rmd_with_plots
Classify Lipids Based on Their Namesclassify_lipids
Convert List Columns to Stringsconvert_list_columns_to_strings
Correct Batch Effects from a Normalised Lipidomics Matrixcorrect_batch_effects
Create Default Contrastscreate_default_contrasts
Create an Enrichment Barplotcreate_enrichment_barplot
Create an Enrichment Dotplotcreate_enrichment_dotplot
Create a Robust Heatmap of Top Variable Featurescreate_heatmap_robust
Create a Lipid Expression Barplot Ordered by Groupcreate_lipid_expression_barplot
Create Pathway Setscreate_pathway_sets
Create a PCA Plot with Optional Confidence or Visual Ellipsescreate_pca_plot_with_ellipses
Quick QC Plot for a Normalized Data Matrixcreate_pipeline_plot
Create a PLS-DA Plot with Optional Ellipsescreate_plsda_plot_with_ellipses
Create a Volcano Plot with Optional Classification Colouringcreate_volcano_plot_labeled
Determine Fatty-Acid Saturation from a Lipid Namedetermine_saturation
Example lipidomics dataset (lazy generator)example_lipidomics_data
Export Lipid Classification to CSVexport_classification
Align Samples Between Data Matrix and Metadatafix_sample_alignment
Generate Example Datasetgenerate_example_data
Return Human-Readable Descriptions of Imputation Methodsget_imputation_descriptions
Return Available Imputation Method Namesget_imputation_methods
Get Lipid Classificationget_lipid_classification
Return Human-Readable Descriptions of Normalization Methodsget_normalization_descriptions
Return Available Normalization Method Namesget_normalization_methods
Impute Missing Values in a Lipidomics Data Matriximpute_missing_values
Launch the LIPIDIFy Shiny Applicationlaunch_lipidomics_app
Load Custom Lipid Classification from a CSV Fileload_custom_classification
Load Custom Enrichment Sets from a CSV Fileload_custom_enrichment_sets
Load Lipidomics Dataload_lipidomics_data
Load Lipidomics Data from Data Frameload_lipidomics_data_from_df
Normalize Lipidomics Datanormalize_lipidomics_data
Log2 Median Centering Normalizationnormalize_log2median normalize_vsn
Mean Normalizationnormalize_mean
Median Normalizationnormalize_median
PQN Normalizationnormalize_pqn
Quantile Normalizationnormalize_quantile
TIC Normalizationnormalize_tic
Perform Differential Analysisperform_differential_analysis
Perform Differential Analysis with EdgeRperform_differential_analysis_edger
Perform Differential Analysis with limmaperform_differential_analysis_limma
Perform Enrichment Analysisperform_enrichment_analysis
Perform PCA Analysisperform_pca
Perform PLS-DA Analysis (FIXED VERSION)perform_plsda
Run FGSEA (original function kept for compatibility)run_fgsea
Run FGSEA with Error Handlingrun_fgsea_safe
Test Saturation Classificationtest_saturation_classification
Visualize Raw Datavisualize_raw_data
Visualize Raw or Normalized Data with Sample/Lipid Togglevisualize_raw_data_improved