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DESCRIPTION
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DESCRIPTION
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Package: tima
Title: Taxonomically Informed Metabolite Annotation
Version: 2.11.0
Authors@R: c(
person("Adriano", "Rutz", , "adafede@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-0443-9902")),
person("Pierre-Marie", "Allard", , "pierre-marie.allard@unifr.ch", role = "ctb",
comment = c(ORCID = "0000-0003-3389-2191"))
)
Maintainer: Adriano Rutz <adafede@gmail.com>
Description: This package provides the infrastructure to perform
Taxonomically Informed Metabolite Annotation.
License: GPL (>= 3)
URL: https://github.com/taxonomicallyinformedannotation/tima,
https://taxonomicallyinformedannotation.github.io/tima,
https://taxonomicallyinformedannotation.github.io/tima-shinylive
BugReports: https://github.com/taxonomicallyinformedannotation/tima/issues
Depends:
R (>= 4.3.0)
Imports:
BiocParallel (>= 1.36.0),
crayon (>= 1.5.3),
docopt (>= 0.7.1),
dplyr (>= 1.1.4),
DT (>= 0.33),
fs (>= 1.6.5),
gt (>= 0.11.1),
httr (>= 1.4.7),
httr2 (>= 1.0.7),
igraph (>= 2.1.2),
jsonlite (>= 1.8.9),
MetaboCoreUtils (>= 1.10.0),
MsBackendMgf (>= 1.10.0),
MsBackendMsp (>= 1.6.0),
msentropy (>= 0.1.4),
purrr (>= 1.0.2),
rotl (>= 3.1.0),
shiny (>= 1.10.0),
shinybusy (>= 0.3.3),
shinyWidgets (>= 0.8.7),
Spectra (>= 1.12.0),
stats,
stringi (>= 1.8.4),
targets (>= 1.9.1),
tidyfst (>= 1.8.1),
tidyselect (>= 1.2.1),
tidytable (>= 0.11.1),
utils,
visNetwork (>= 2.1.2),
yaml (>= 2.3.10)
Suggests:
BiocManager,
knitr,
lifecycle,
pkgload,
R.utils,
rlang,
shinyhelper,
shinyjs,
shinytest2,
shinyvalidate,
spelling,
testthat (>= 3.0.0)
VignetteBuilder:
knitr
biocViews: metabolite annotation, chemotaxonomy, scoring system, natural
products, computational metabolomics, taxonomic distance, specialized
metabolome
ByteCompile: true
Config/Needs/website: rmarkdown
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
X-schema.org-keywords: metabolite annotation, chemotaxonomy, scoring
system, natural products, computational metabolomics, taxonomic
distance, specialized metabolome
Collate:
'round_reals.R'
'log_pipe.R'
'harmonize_adducts.R'
'parse_yaml_params.R'
'parse_cli_params.R'
'get_default_paths.R'
'get_params.R'
'dist_groups.R'
'decorate_masses.R'
'parse_adduct.R'
'calculate_mass_of_m.R'
'annotate_masses.R'
'sanitize_spectra.R'
'import_spectra.R'
'annotate_spectra.R'
'benchmark_taxize_spectra.R'
'calculate_entropy_score.R'
'load_yaml_files.R'
'go_to_cache.R'
'create_dir.R'
'change_params_small.R'
'clean_bio.R'
'filter_high_confidence_only.R'
'columns_model.R'
'clean_collapse.R'
'clean_chemo.R'
'complement_metadata_structures.R'
'copy_backbone.R'
'create_components.R'
'create_edges.R'
'create_edges_spectra.R'
'decorate_bio.R'
'decorate_chemo.R'
'export_output.R'
'export_params.R'
'export_spectra_rds.R'
'extract_spectra.R'
'fake_annotations_columns.R'
'fake_ecmdb.R'
'fake_hmdb.R'
'fake_lotus.R'
'fake_sop_columns.R'
'filter_annotations.R'
'get_file.R'
'get_example_sirius.R'
'get_example_files.R'
'get_gnps_tables.R'
'get_last_version_from_zenodo.R'
'get_massbank_spectra.R'
'get_organism_taxonomy_ott.R'
'globals.R'
'harmonize_names_sirius.R'
'harmonize_spectra.R'
'install.R'
'log_debug.R'
'pre_harmonize_names_sirius.R'
'select_annotations_columns.R'
'prepare_annotations_gnps.R'
'select_sirius_columns.R'
'read_from_sirius_zip.R'
'prepare_annotations_sirius.R'
'prepare_annotations_spectra.R'
'prepare_features_components.R'
'prepare_features_edges.R'
'prepare_features_tables.R'
'prepare_libraries_rt.R'
'select_sop_columns.R'
'prepare_libraries_sop_closed.R'
'prepare_libraries_sop_ecmdb.R'
'prepare_libraries_sop_hmdb.R'
'prepare_libraries_sop_lotus.R'
'split_tables_sop.R'
'prepare_libraries_sop_merged.R'
'prepare_libraries_spectra.R'
'prepare_params.R'
'prepare_taxa.R'
'replace_id.R'
'run_app.R'
'tima-package.R'
'tima_full.R'
'transform_score_sirius_csi.R'
'weight_chemo.R'
'weight_bio.R'
'weight_annotations.R'