Package: MetMashR
Type: Package
Title: Metabolite Mashing with R
Version: 1.0.0
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: 7.3.1
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_upset_chart_class.R' 'annotation_venn_chart.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' 'openbabel_structure_chart.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, ChemmineOB, rsvg, metabolomicsWorkbenchR, KEGGREST,
        plyr, magick, structToolbox, RVenn, ggVennDiagram, patchwork,
        XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset,
        jsonlite, openxlsx
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
git_url: https://git.bioconductor.org/packages/MetMashR
git_branch: RELEASE_3_20
git_last_commit: 5ccb773
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-30 03:57:00 UTC; biocbuild
Author: Gavin Rhys Lloyd [aut, cre] (<https://orcid.org/0000-0001-7989-6695>),
  Ralf Johannes Maria Weber [aut]
Maintainer: Gavin Rhys Lloyd <g.r.lloyd@bham.ac.uk>
Built: R 4.4.1; ; 2024-10-30 16:14:19 UTC; windows
