Package: metabolomicsWorkbenchR 1.17.0

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]

# Install 'metabolomicsWorkbenchR' in R:

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

On BioConductor:metabolomicsWorkbenchR-1.17.0(bioc 3.21)metabolomicsWorkbenchR-1.16.0(bioc 3.20)

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

software metabolomics

4.60 score 8 scripts 204 downloads 10 exports 61 dependencies

Last updated 2 months agofrom:3a7c45842e. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 08 2024
R-4.5-win	NOTE	Dec 08 2024
R-4.5-linux	NOTE	Dec 08 2024
R-4.4-win	NOTE	Dec 08 2024
R-4.4-mac	NOTE	Dec 08 2024
R-4.3-win	NOTE	Dec 08 2024
R-4.3-mac	NOTE	Dec 08 2024

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 crayon curl data.table DelayedArray dplyr evaluate fansi generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue highr httr httr2 IRanges jsonlite knitr lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime MultiAssayExperiment ontologyIndex openssl pillar pkgconfig purrr R6 rappdirs rlang rols S4Arrays S4Vectors SparseArray stringi stringr struct SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr xfun XVector yaml zlibbioc

Example using structToolbox

Gavin R Lloyd, Ralf J Weber

Rendered fromexample_using_structToolbox.Rmdusingknitr::rmarkdownon Dec 08 2024.

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

Introduction to metabolomicsWorkbenchR

Gavin R Lloyd, Ralf J Weber

Rendered fromIntroduction_to_metabolomicsWorkbenchR.Rmdusingknitr::rmarkdownon Dec 08 2024.

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