Package: lipidr 2.21.0

Ahmed Mohamed

lipidr: Data Mining and Analysis of Lipidomics Datasets

lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation.

Authors:Ahmed Mohamed [cre], Ahmed Mohamed [aut], Jeffrey Molendijk [aut]

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lipidr.pdf |lipidr.html✨
lipidr/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/ahmohamed/lipidr/issues

On BioConductor:lipidr-2.21.0(bioc 3.21)lipidr-2.20.0(bioc 3.20)

lipidomicsmassspectrometrynormalizationqualitycontrolvisualizationbioconductor

7.44 score 29 stars 40 scripts 308 downloads 6 mentions 44 exports 117 dependencies

Last updated 3 months agofrom:ce50d7045a. Checks:1 OK, 6 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 20 2025
R-4.5-winERRORJan 20 2025
R-4.5-linuxERRORJan 20 2025
R-4.4-winERRORJan 20 2025
R-4.4-macERRORJan 20 2025
R-4.3-winERRORJan 20 2025
R-4.3-macERRORJan 20 2025

Exports:.LipidomicsExperiment%>%add_sample_annotationannotate_lipidsas_lipidomics_experimentde_analysisde_designfetch_mw_studyfilter_by_cvgen_lipidsetsimpute_nais_loggedis_normalizedis_summarizedLipidomicsExperimentlist_mw_studieslseamvanon_parsed_moleculesnormalize_istdnormalize_pqnplot_chain_distributionplot_class_enrichmentplot_enrichmentplot_lipidclassplot_moleculesplot_mvaplot_mva_loadingsplot_results_volcanoplot_samplesplot_trendread_mw_datamatrixread_mwTabread_skylineremove_non_parsed_moleculesset_loggedset_normalizedset_summarizedsignificant_lipidsetssignificant_moleculessummarize_transitionstop_lipidsupdate_molecule_namesuse_interactive_graphics

Dependencies:abindaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcalibrateclicodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrevaluatefansifarverfastmapfastmatchfgseafontawesomeforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegmmgtablehighrhtmltoolshtmlwidgetshttrimputeimputeLCMDIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentMultiDataSetmunsellmvtnormnlmenormopensslpcaMethodspillarpkgconfigplotlypromisespurrrqqmanR6rappdirsRColorBrewerRcpprlangrmarkdownroplsS4ArraysS4VectorssandwichsassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextmvtnormUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzoo

Workflow

Ahmed Mohamed

Rendered fromworkflow.Rmdusingknitr::rmarkdownon Jan 20 2025.

Last update: 2020-09-30
Started: 2019-02-26

Readme and manuals

Help Manual

Help pageTopics
Add sample annotation to Skyline data frameadd_sample_annotation
Parse molecule names to extract lipid class and chain information.annotate_lipids
Convert data.frame/matrix to LipidomicsExperimentas_lipidomics_experiment
Differential analysis of lipids between sample groupsde_analysis de_design plot_results_volcano significant_molecules
Remove molecules with CV larger that a thresholdfilter_by_cv
Generate lipid sets from lipid molecule namesgen_lipidsets
Impute missing values in a LipidomicsExperimentimpute_na
Functions to get and set attributes of LipidomicsExperiment objectsis_logged is_normalized is_summarized set_logged set_normalized set_summarized
Constructor for Lipidomics experiment from list of assaysLipidomicsExperiment
LipidomicsExperiment object.LipidomicsExperiment LipidomicsExperiment-class
Metabolomics Workbench integrationfetch_mw_study list_mw_studies read_mwTab read_mw_datamatrix
Lipid set enrichment analysis (LSEA)lsea plot_class_enrichment plot_enrichment significant_lipidsets
Perform multivariate analyses to investigate sample clusteringmva plot_mva plot_mva_loadings top_lipids
Get a list of molecules that couldn't be parsed by 'lipidr'non_parsed_molecules
Normalize each class by its corresponding internal standard(s).normalize_istd
Perform Probabilistic Quotient Normalization for intensities.normalize_pqn
Plot logFC of lipids per class showing chain informationplot_chain_distribution
Informative plots to investigate lipid classesplot_lipidclass
Informative plots to investigate individual lipid moleculesplot_molecules
Informative plots to investigate samplesplot_samples
Plot a regulation trend line between logFC and chain annotationplot_trend
Read Skyline exported filesread_skyline
Remove molecules that couldn't be parsed by 'lipidr' from the datasetremove_non_parsed_molecules
Summarize transitionssummarize_transitions
Rename molecules in a dataset.update_molecule_names
Activate interactive graphicsuse_interactive_graphics