Package: MetMashR
Type: Package
Title: Metabolite Mashing with R
Version: 1.5.0
Authors@R: c(
    person(
        c("Gavin","Rhys"),
          "Lloyd",
           role=c("aut","cre"),
           email="g.r.lloyd@bham.ac.uk",
		   comment = c(ORCID = "0000-0001-7989-6695")
		),
    person(
        c("Ralf","Johannes", "Maria"),
          "Weber",
           role=c("aut"),
           email="r.j.weber@bham.ac.uk")
        )
Description: A package to merge, filter sort, organise and otherwise
        mash together metabolite annotation tables. Metabolite
        annotations can be imported from multiple sources (software)
        and combined using workflow steps based on S4 class templates
        derived from the `struct` package. Other modular workflow steps
        such as filtering, merging, splitting, normalisation and
        rest-api queries are included.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.3
Depends: R (>= 4.3.0), struct
Imports: dplyr, methods, httr, scales, ggthemes, ggplot2, utils, rlang,
        cowplot, stats
Collate: 'generics.R' 'zzz.R' 'annotation_source_class.R'
        'annotation_database_class.R' 'AnnotationDb_database.R'
        'AnnotationDb_select_class.R'
        'BiocFileCache_database_helpers.R'
        'BiocFileCache_database_class.R' 'CompoundDb_source_class.R'
        'MTox700plus_database_class.R' 'MetMashR-package.R'
        'PathBank_metabolite_database_class.R' 'add_columns_class.R'
        'add_labels_class.R' 'annotation_bar_chart.R'
        'annotation_histogram_class.R' 'annotation_histogram2d_class.R'
        'annotation_pie_chart.R' 'annotation_table_class.R'
        'annotation_venn_chart.R' 'annotation_upset_chart_class.R'
        'calc_ppm_diff_class.R' 'calc_rt_diff_class.R'
        'lcms_table_class.R' 'cd_source_class.R' 'chart_plot_doc.R'
        'rest_api_parsers.R' 'rest_api_class.R'
        'classyfire_lookup_class.R' 'combine_columns_class.R'
        'combine_records_class.R' 'combine_sources.R'
        'compute_column_class.R' 'compute_record_class.R'
        'database_lookup_class.R' 'dictionaries.R'
        'eutils_lookup_class.R' 'excel_database_class.R'
        'expand_records_class.R' 'filter_labels_class.R'
        'filter_na_class.R' 'filter_range_class.R'
        'filter_records_class.R' 'filter_venn_class.R'
        'github_file_class.R' 'go_database_class.R'
        'hmdb_lookup_class.R' 'id_count_class.R'
        'import_source_class.R' 'kegg_lookup_class.R'
        'lipidmaps_lookup_class.R' 'ls_source_class.R'
        'model_apply_doc.R' 'mspurity_source_class.R'
        'mwb_compound_lookup_class.R' 'mwb_refmet_database_class.R'
        'mwb_structure_chart_class.R' 'mz_match_class.R'
        'mzrt_match_class.R' 'normalise_lipids_class.R'
        'normalise_strings_class.R' 'opsin_lookup_class.R'
        'pivot_columns_class.R' 'prioritise_columns_class.R'
        'pubchem_compound_lookup_class.R'
        'pubchem_property_lookup_class.R'
        'pubchem_structure_chart_class.R'
        'pubchem_structure_lookup_class.R' 'pubchem_widget.R'
        'rdata_database_class.R' 'rds_database_class.R'
        'rds_cache_class.R' 'remove_columns_class.R'
        'rename_columns_class.R' 'rt_match_class.R'
        'select_columns_class.R' 'split_column_class.R'
        'sqlite_database_class.R' 'trim_whitespace_class.R'
        'unique_records_class.R'
Suggests: covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0),
        rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache,
        msPurity, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick,
        structToolbox, ggVennDiagram, patchwork, XML, GO.db, tidytext,
        tidyr, tidyselect, ComplexUpset, jsonlite, openxlsx, ggplotify
Config/testthat/edition: 3
VignetteBuilder: knitr
URL: https://computational-metabolomics.github.io/MetMashR/
Roxygen: list(markdown = TRUE)
biocViews: WorkflowStep, Metabolomics, KEGG
BugReports: https://github.com/computational-metabolomics/MetMashR/issues
Config/pak/sysreqs: libicu-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:32:41 UTC
RemoteUrl: https://github.com/bioc/MetMashR
RemoteRef: HEAD
RemoteSha: 9dbb552679349e9f787dcb7bd6ee2849f0861767
NeedsCompilation: no
Packaged: 2026-02-01 08:47:38 UTC; root
Author: Gavin Rhys Lloyd [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7989-6695>),
  Ralf Johannes Maria Weber [aut]
Maintainer: Gavin Rhys Lloyd <g.r.lloyd@bham.ac.uk>
Built: R 4.6.0; ; 2026-02-01 08:50:30 UTC; windows
