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✨
DESCRIPTION |NEWS
card.svg |card.png
metabolomicsWorkbenchR/json (API)

# 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.

softwaremetabolomics

4.41 score 13 scripts 10 exports 54 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksNOTE193
linux-devel-x86_64NOTE372
source / vignettesOK287
linux-release-x86_64NOTE330
macos-release-arm64NOTE220
macos-oldrel-arm64NOTE214
windows-develNOTE215
windows-releaseNOTE231
windows-oldrelNOTE229
wasm-releaseOK182

Exports:check_patterncheck_putscontextcontext_inputscontext_outputsdo_queryinput_exampleinput_itemis_validoutput_item

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericsclicpp11curldata.tableDelayedArraydplyrevaluategenericsGenomicRangesgluehighrhttrhttr2IRangesjsonliteknitrlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeMultiAssayExperimentopensslpillarpkgconfigpurrrR6rappdirsrlangS4ArraysS4VectorsSeqinfoSparseArraystringistringrstructSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrxfunXVectoryaml

Example using structToolbox
Introduction | Installation | Querying the database | Choosing a study | Workflow | Session Info
Rendered fromexample_using_structToolbox.Rmdusingknitr::rmarkdown

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

Introduction to metabolomicsWorkbenchR
Introduction | Installation | Running a query | Special cases | input_item "ignored" | output_item "compound_exact", "protein_exact" and "gene_exact" | output_item "protein_partial" and "gene_partial" | output_item "SummarizedExperiment" and "DatasetExperiment" | output_item "MultiAssayExperiment" | output_item "untarg_SummarizedExperiment" and "untarg_DatasetExperiment" | S4 classes | Contexts | Input / Output Items | Session Info
Rendered fromIntroduction_to_metabolomicsWorkbenchR.Rmdusingknitr::rmarkdown

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

Readme and manuals

Help Manual

Help pageTopics
Get slot value from mw_base objects$,mw_base-method
Check input against acceptable input patterncheck_pattern check_pattern,mw_input_item-method
Check inputs/outputs matchcheck_puts check_puts,mw_input_item-method
Contextscontext
Valid inputscontext_inputs
Valid outputscontext_outputs
Query the Metabolomics Workbench databasedo_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_iteminput_example
Input itemsinput_item
Check validity of context and inputs/outputsis_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 itemsoutput_item