Package: MWASTools 1.29.0

Andrea Rodriguez-Martinez

MWASTools: MWASTools: an integrated pipeline to perform metabolome-wide association studies

MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.

Authors:Andrea Rodriguez-Martinez, Joram M. Posma, Rafael Ayala, Ana L. Neves, Maryam Anwar, Jeremy K. Nicholson, Marc-Emmanuel Dumas

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NEWS

# Install 'MWASTools' in R:

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

Datasets:

KEGG_metabolic_paths - KEGG human metabolic pathways
MS_data - Simulated LC-MS features
metabo_SE - NMR plasma metabolic profiles dataset
targetMetabo_SE - Target NMR metabolites dataset

On BioConductor:MWASTools-1.29.0(bioc 3.20)MWASTools-1.28.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

23 exports 1.08 score 112 dependencies 1 dependents 1 mentions

Last updated 2 months agofrom:abf4ef05ab

Exports:CV_filter JBA_binning JBA_corDistribution JBA_plotBins MWAS_barplot MWAS_bootstrapping MWAS_filter MWAS_heatmap MWAS_KEGG_network MWAS_KEGG_pathways MWAS_KEGG_shortestpaths MWAS_network MWAS_scatterplotMS MWAS_skylineNMR MWAS_stats MWAS_SummarizedExperiment plot_spectraNMR QC_CV QC_CV_scatterplot QC_CV_specNMR QC_PCA QC_PCA_scoreplot STOCSY_NMR

Dependencies:abind askpass backports Biobase BiocGenerics Biostrings bitops boot broom car carData circlize cli clue cluster codetools colorspace ComplexHeatmap cowplot cpp11 crayon curl DelayedArray Deriv digest doBy doParallel dplyr fansi farver foreach generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggplot2 glm2 GlobalOptions glue graph gridExtra gtable httr igraph IRanges isoband iterators jsonlite KEGGgraph KEGGREST labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv microbenchmark mime minqa modelr munsell nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig plyr png ppcor purrr quantreg qvalue R6 RColorBrewer Rcpp RcppEigen RCurl reshape2 Rgraphviz rjson rlang S4Arrays S4Vectors scales shape SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector zlibbioc

MWASTools

Rendered fromMWASTools.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2018-09-06
Started: 2016-11-28

Help page	Topics
Filter metabolic data by CV	CV_filter
Binning of pJRES spectra	JBA_binning
Setting the ct threshold for JBA	JBA_corDistribution
Visualization of JBA bins	JBA_plotBins
KEGG human metabolic pathways	KEGG_metabolic_paths
NMR plasma metabolic profiles dataset	metabo_SE
Simulated LC-MS features	MS_data
Visualize MWAS results in a bar plot	MWAS_barplot
MWAS bootstrap resampling	MWAS_bootstrapping
Filter MWAS results by p-value and/or CV	MWAS_filter
Visualize MWAS results as a multiple-phenotype heatmap	MWAS_heatmap
Build a KEGG-based metabolic network	MWAS_KEGG_network
Map metabolites into KEGG pathways	MWAS_KEGG_pathways
Build a shortest-path metabolic subnetwork	MWAS_KEGG_shortestpaths
Visualize MWAS results in a correlation-based metabolic network	MWAS_network
Visualize MWAS results in MS-based scatter plot	MWAS_scatterplotMS
Visualize MWAS results in an NMR-skyline plot	MWAS_skylineNMR
Metabolome-Wide Associations	MWAS_stats
Create a SummarizeExperiment object	MWAS_SummarizedExperiment
Plot NMR spectra	plot_spectraNMR
Calculate coefficients of variation	QC_CV
Plot MS-based scatter plot colored based on CV	QC_CV_scatterplot
Plot NMR spectrum colored based on CV	QC_CV_specNMR
Principal Component Analysis	QC_PCA
PCA score plot	QC_PCA_scoreplot
Statistical Total Correlation Spectroscopy - Academic use only	STOCSY_NMR
Target NMR metabolites dataset	targetMetabo_SE

Package: MWASTools 1.29.0

MWASTools: MWASTools: an integrated pipeline to perform metabolome-wide association studies

MWASTools

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