Package: lipidr 2.19.0

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

Datasets:

    On BioConductor:lipidr-2.19.0(bioc 3.20)lipidr-2.18.0(bioc 3.19)

    bioconductor-package

    44 exports 0.71 score 118 dependencies 6 mentions

    Last updated 2 months agofrom:562b70e98e

    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.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioczoo

    Workflow

    Ahmed Mohamed

    Rendered fromworkflow.Rmdusingknitr::rmarkdownon Jun 30 2024.

    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