Package: metabolomicsWorkbenchR 1.23.0

Gavin Rhys Lloyd

metabolomicsWorkbenchR: Metabolomics Workbench in R

This package provides functions for interfacing with the Metabolomics Workbench RESTful API. Study, compound, protein and gene information can be searched for using the API. Methods to obtain study data in common Bioconductor formats such as SummarizedExperiment and MultiAssayExperiment are also included.

Authors:Gavin Rhys Lloyd [aut, cre], Ralf Johannes Maria Weber [aut]

metabolomicsWorkbenchR_1.23.0.tar.gz
metabolomicsWorkbenchR_1.23.0.zip(r-4.7)metabolomicsWorkbenchR_1.23.0.zip(r-4.6)metabolomicsWorkbenchR_1.23.0.zip(r-4.5)
metabolomicsWorkbenchR_1.23.0.tgz(r-4.6-any)metabolomicsWorkbenchR_1.23.0.tgz(r-4.5-any)
metabolomicsWorkbenchR_1.23.0.tar.gz(r-4.7-any)metabolomicsWorkbenchR_1.23.0.tar.gz(r-4.6-any)
metabolomicsWorkbenchR_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
metabolomicsWorkbenchR/json (API)
NEWS

# Install 'metabolomicsWorkbenchR' in R:

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

On BioConductor:metabolomicsWorkbenchR-1.23.0(bioc 3.24)metabolomicsWorkbenchR-1.22.0(bioc 3.23)

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

software metabolomics

4.41 score 13 scripts 392 downloads 10 exports 54 dependencies

Last updated from:5bac27b0d1. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	214
linux-devel-x86_64	NOTE	407
source / vignettes	OK	258
linux-release-x86_64	NOTE	374
macos-release-arm64	NOTE	196
macos-oldrel-arm64	NOTE	197
windows-devel	NOTE	228
windows-release	NOTE	264
windows-oldrel	NOTE	204
wasm-release	OK	143

Exports:check_pattern check_puts context context_inputs context_outputs do_query input_example input_item is_valid output_item

Dependencies:abind askpass Biobase BiocBaseUtils BiocGenerics cli cpp11 curl data.table DelayedArray dplyr evaluate generics GenomicRanges glue highr httr httr2 IRanges jsonlite knitr lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime MultiAssayExperiment openssl pillar pkgconfig purrr R6 rappdirs rlang S4Arrays S4Vectors Seqinfo SparseArray stringi stringr struct SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr xfun XVector yaml

Example using structToolbox

Gavin R Lloyd, Ralf J Weber

Rendered fromexample_using_structToolbox.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-09-25
Started: 2021-02-23

Introduction to metabolomicsWorkbenchR

Gavin R Lloyd, Ralf J Weber

Rendered fromIntroduction_to_metabolomicsWorkbenchR.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-09-25
Started: 2020-06-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get slot value from mw_base objects	$,mw_base-method
Check input against acceptable input pattern	check_pattern check_pattern,mw_input_item-method
Check inputs/outputs match	check_puts check_puts,mw_input_item-method
Contexts	context
Valid inputs	context_inputs
Valid outputs	context_outputs
Query the Metabolomics Workbench database	do_query do_query,character,character,character,character-method do_query,character,character,character,missing-method do_query,mw_context,mw_input_item,character,mw_DE_item-method do_query,mw_context,mw_input_item,character,mw_MAE_item-method do_query,mw_context,mw_input_item,character,mw_output_item-method do_query,mw_context,mw_input_item,character,mw_SE_item-method do_query,mw_context,mw_input_item,character,mw_untarg_DE_item-method do_query,mw_context,mw_input_item,character,mw_untarg_SE_item-method do_query,mw_exactmass_context,character,character,missing-method do_query,mw_exactmass_context,list,character,character-method do_query,mw_exactmass_context,list,character,missing-method do_query,mw_exactmass_context,list,character,mw_output_item-method do_query,mw_moverz_context,character,character,missing-method do_query,mw_moverz_context,list,character,character-method do_query,mw_moverz_context,list,character,missing-method do_query,mw_moverz_context,list,character,mw_output_item-method
Valid input_value for input_item	input_example
Input items	input_item
Check validity of context and inputs/outputs	is_valid is_valid,mw_context,character,character,character-method is_valid,mw_exactmass_context,character,character,missing-method is_valid,mw_moverz_context,character,character,missing-method
Output items	output_item