Package: LIPIDIFy 0.99.7

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], Karen Sheppard [fnd]

LIPIDIFy_0.99.7.tar.gz
LIPIDIFy_0.99.7.zip(r-4.7-any)LIPIDIFy_0.99.7.zip(r-4.6-any)LIPIDIFy_0.99.7.zip(r-4.5-any)
LIPIDIFy_0.99.7.tgz(r-4.6-any)LIPIDIFy_0.99.7.tgz(r-4.5-any)
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LIPIDIFy_0.99.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LIPIDIFy/json (API)

# Install 'LIPIDIFy' in R:

install.packages('LIPIDIFy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

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

On BioConductor:LIPIDIFy-0.99.7(bioc 3.24)

software lipidomics massspectrometry normalization preprocessing differentialexpression genesetenrichment visualization shinyapps multiplecomparison batcheffect qualitycontrol dataimport classification

4.74 score 1 stars 94 downloads 40 exports 143 dependencies

Last updated from:69e5b6746d. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	190
linux-devel	OK	364
source / vignettes	OK	462
linux-release	OK	397
macos-release	OK	162
macos-oldrel	OK	229
windows-devel	OK	352
windows-release	OK	335
windows-oldrel	OK	232
wasm-release	OK	158

Exports:apply_normalizations classify_lipids correct_batch_effects create_default_contrasts create_enrichment_barplot create_enrichment_dotplot create_heatmap_robust create_lipid_expression_barplot create_pca_plot_with_ellipses create_pipeline_plot create_plsda_plot_with_ellipses create_volcano_plot_labeled determine_saturation export_classification fix_sample_alignment generate_example_data get_imputation_descriptions get_imputation_methods get_normalization_descriptions get_normalization_methods impute_missing_values launch_lipidomics_app load_custom_classification load_custom_enrichment_sets load_lipidomics_data load_lipidomics_data_from_df normalize_log2median normalize_mean normalize_median normalize_pqn normalize_quantile normalize_tic normalize_vsn perform_differential_analysis perform_enrichment_analysis perform_pca perform_plsda test_saturation_classification visualize_raw_data visualize_raw_data_improved

Dependencies:abind askpass backports base64enc BH BiocParallel boot broom bslib cachem car carData cli cluster codetools colorspace commonmark cowplot cpp11 crosstalk curl data.table Deriv digest doBy dplyr DT edgeR ellipse emmeans estimability evaluate FactoMineR farver fastmap fastmatch fgsea flashClust fontawesome forecast formatR Formula fracdiff fs futile.logger futile.options generics ggplot2 ggrepel glue gridExtra gtable highr htmltools htmlwidgets httpuv httr irlba isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 lmtest locfit magrittr MASS Matrix MatrixModels memoise mgcv mime minqa modelr multcompView mvtnorm nlme nloptr nnet numDeriv openssl openxlsx otel pbkrtest pheatmap pillar pkgconfig plotly pls promises purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown S7 sass scales scatterplot3d shiny shinydashboard showtext showtextdb snow sourcetools SparseM statmod stringi stringr survival sys sysfonts tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridisLite withr xfun xtable yaml zip zoo

LIPIDIFy

Rendered fromLIPIDIFy.Rmdusingknitr::rmarkdown

Last update: 2026-09-23
Started: 2026-07-21

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

Package: LIPIDIFy 0.99.7

LIPIDIFy: Comprehensive Lipidomics Data Analysis with Interactive Visualization

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