Package: lipidr 2.27.0

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]

lipidr_2.27.0.tar.gz
lipidr_2.27.0.zip(r-4.7)lipidr_2.27.0.zip(r-4.6)lipidr_2.27.0.zip(r-4.5)
lipidr_2.27.0.tgz(r-4.6-any)lipidr_2.27.0.tgz(r-4.5-any)
lipidr_2.27.0.tar.gz(r-4.7-any)lipidr_2.27.0.tar.gz(r-4.6-any)
lipidr_2.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lipidr/json (API)

# Install 'lipidr' in R:

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

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

On BioConductor:lipidr-2.27.0(bioc 3.24)lipidr-2.26.0(bioc 3.23)

lipidomics massspectrometry normalization qualitycontrol visualization bioconductor

8.06 score 33 stars 145 scripts 6 mentions 44 exports 111 dependencies

Last updated from:f3726e3a90. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	211
linux-devel-x86_64	ERROR	531
source / vignettes	OK	295
linux-release-x86_64	ERROR	377
macos-release-arm64	ERROR	245
macos-oldrel-arm64	ERROR	208
windows-devel	ERROR	463
windows-release	ERROR	449
windows-oldrel	ERROR	502
wasm-release	OK	187

Exports:.LipidomicsExperiment %>%add_sample_annotation annotate_lipids as_lipidomics_experiment de_analysis de_design fetch_mw_study filter_by_cv gen_lipidsets impute_na is_logged is_normalized is_summarized LipidomicsExperiment list_mw_studies lsea mva non_parsed_molecules normalize_istd normalize_pqn plot_chain_distribution plot_class_enrichment plot_enrichment plot_lipidclass plot_molecules plot_mva plot_mva_loadings plot_results_volcano plot_samples plot_trend read_mw_datamatrix read_mwTab read_skyline remove_non_parsed_molecules set_logged set_normalized set_summarized significant_lipidsets significant_molecules summarize_transitions top_lipids update_molecule_names use_interactive_graphics

Dependencies:abind askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel bslib cachem calibrate cli codetools cowplot cpp11 crosstalk curl data.table DelayedArray digest dplyr evaluate farver fastmap fastmatch fgsea fontawesome forcats formatR fs futile.logger futile.options generics GenomicRanges ggplot2 ggrepel glue gmm gtable highr htmltools htmlwidgets httr impute imputeLCMD IRanges isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment MultiDataSet mvtnorm norm openssl otel pcaMethods pillar pkgconfig plotly promises purrr qqman R6 rappdirs RColorBrewer Rcpp rlang rmarkdown ropls S4Arrays S4Vectors S7 sandwich sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tmvtnorm utf8 vctrs viridisLite withr xfun XVector yaml zoo

Workflow

Rendered fromworkflow.Rmdusingknitr::rmarkdown

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

Help page	Topics
Add sample annotation to Skyline data frame	add_sample_annotation
Parse molecule names to extract lipid class and chain information.	annotate_lipids
Convert data.frame/matrix to LipidomicsExperiment	as_lipidomics_experiment
Differential analysis of lipids between sample groups	de_analysis de_design plot_results_volcano significant_molecules
Remove molecules with CV larger that a threshold	filter_by_cv
Generate lipid sets from lipid molecule names	gen_lipidsets
Impute missing values in a LipidomicsExperiment	impute_na
Functions to get and set attributes of LipidomicsExperiment objects	is_logged is_normalized is_summarized set_logged set_normalized set_summarized
Constructor for Lipidomics experiment from list of assays	LipidomicsExperiment
LipidomicsExperiment object	.LipidomicsExperiment LipidomicsExperiment-class
Metabolomics Workbench integration	fetch_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 clustering	mva 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 information	plot_chain_distribution
Informative plots to investigate lipid classes	plot_lipidclass
Informative plots to investigate individual lipid molecules	plot_molecules
Informative plots to investigate samples	plot_samples
Plot a regulation trend line between logFC and chain annotation	plot_trend
Read Skyline exported files	read_skyline
Remove molecules that couldn't be parsed by 'lipidr' from the dataset	remove_non_parsed_molecules
Summarize transitions	summarize_transitions
Rename molecules in a dataset.	update_molecule_names
Activate interactive graphics	use_interactive_graphics

Package: lipidr 2.27.0

lipidr: Data Mining and Analysis of Lipidomics Datasets

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)