bioc-issue-bot
commented
2 hours ago Hi @grlloyd
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: MetMashR
Type: Package
Title: Metabolite Mashing with R
Version: 0.99.0
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
LazyData: false
RoxygenNote: 7.3.1
Depends:
R (>= 4.3.0),
struct
Imports:
dplyr,
methods,
jsonlite,
openxlsx,
httr,
scales,
ggthemes,
ggplot2,
utils,
rlang,
cowplot
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'
'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'
'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
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
grlloyd
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