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:
metabolomicsWorkbenchR_1.17.0.tar.gz
metabolomicsWorkbenchR_1.17.0.zip(r-4.5)metabolomicsWorkbenchR_1.17.0.zip(r-4.4)metabolomicsWorkbenchR_1.17.0.zip(r-4.3)
metabolomicsWorkbenchR_1.17.0.tgz(r-4.4-any)metabolomicsWorkbenchR_1.17.0.tgz(r-4.3-any)
metabolomicsWorkbenchR_1.17.0.tar.gz(r-4.5-noble)metabolomicsWorkbenchR_1.17.0.tar.gz(r-4.4-noble)
metabolomicsWorkbenchR_1.17.0.tgz(r-4.4-emscripten)metabolomicsWorkbenchR_1.17.0.tgz(r-4.3-emscripten)
metabolomicsWorkbenchR.pdf |metabolomicsWorkbenchR.html✨
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-1.17.0(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.
Last updated 23 days agofrom:3a7c45842e. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 08 2024 |
| R-4.5-win | WARNING | Nov 08 2024 |
| R-4.5-linux | WARNING | Nov 08 2024 |
| R-4.4-win | WARNING | Nov 08 2024 |
| R-4.4-mac | NOTE | Nov 08 2024 |
| R-4.3-win | WARNING | Nov 08 2024 |
| R-4.3-mac | NOTE | Nov 08 2024 |
Exports:check_patterncheck_putscontextcontext_inputscontext_outputsdo_queryinput_exampleinput_itemis_validoutput_item
Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericsclicpp11crayoncurldata.tableDelayedArraydplyrevaluatefansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhttrhttr2IRangesjsonliteknitrlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeMultiAssayExperimentontologyIndexopensslpillarpkgconfigpurrrR6rappdirsrlangrolsS4ArraysS4VectorsSparseArraystringistringrstructSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrxfunXVectoryamlzlibbioc
Example using structToolbox
Rendered fromexample_using_structToolbox.Rmdusingknitr::rmarkdownon Nov 08 2024.Last update: 2023-09-25
Started: 2021-02-23
Introduction to metabolomicsWorkbenchR
Rendered fromIntroduction_to_metabolomicsWorkbenchR.Rmdusingknitr::rmarkdownon Nov 08 2024.Last update: 2023-09-25
Started: 2020-06-19
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 |
