Files in taxonomicallyinformedannotation/tima-r
Taxonomically Informed Metabolite Annotation

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CITATION.cff

DESCRIPTION

Dockerfile

LICENSE.md

NAMESPACE

NEWS.md R/annotate_masses.R R/annotate_spectra.R R/benchmark_taxize_spectra.R R/calculate_entropy.R R/calculate_mass_of_m.R R/change_params_small.R R/clean_bio.R R/clean_chemo.R R/clean_collapse.R R/columns_model.R R/complement_metadata_structures.R R/copy_backbone.R R/create_components.R R/create_dir.R R/create_edges.R R/create_edges_spectra.R R/decorate_bio.R R/decorate_chemo.R R/decorate_masses.R R/dist_groups.R R/export_output.R R/export_params.R R/export_spectra_rds.R R/extract_spectra.R R/fake_annotations_columns.R R/fake_ecmdb.R R/fake_hmdb.R R/fake_lotus.R R/fake_sop_columns.R R/filter_annotations.R R/filter_high_confidence_only.R R/get_default_paths.R R/get_example_files.R R/get_example_sirius.R R/get_file.R R/get_gnps_tables.R R/get_last_version_from_zenodo.R R/get_massbank_spectra.R R/get_organism_taxonomy_ott.R R/get_params.R R/globals.R R/go_to_cache.R R/harmonize_adducts.R R/harmonize_names_sirius.R R/harmonize_spectra.R R/import_spectra.R R/install.R R/load_yaml_files.R R/log_debug.R R/log_pipe.R R/parse_adduct.R R/parse_cli_params.R R/parse_yaml_params.R R/pre_harmonize_names_sirius.R R/prepare_annotations_gnps.R R/prepare_annotations_sirius.R R/prepare_annotations_spectra.R R/prepare_features_components.R R/prepare_features_edges.R R/prepare_features_tables.R R/prepare_libraries_rt.R R/prepare_libraries_sop_closed.R R/prepare_libraries_sop_ecmdb.R R/prepare_libraries_sop_hmdb.R R/prepare_libraries_sop_lotus.R R/prepare_libraries_sop_merged.R R/prepare_libraries_spectra.R R/prepare_params.R R/prepare_taxa.R R/read_from_sirius_zip.R R/replace_id.R R/round_reals.R R/run_app.R R/sanitize_spectra.R R/select_annotations_columns.R R/select_sirius_columns.R R/select_sop_columns.R R/split_tables_sop.R R/tima-package.R R/tima_full.R R/transform_score_sirius_csi.R R/weight_annotations.R R/weight_bio.R R/weight_chemo.R README.Rmd README.md

_pkgdown.yml

codecov.yml

codemeta.json

cran-comments.md

data/.gitignore

docker-compose.yml

inst/CITATION

inst/WORDLIST

inst/_targets.R inst/app.R

inst/params/.gitignore

inst/params/default/annotate_masses.yaml

inst/params/default/annotate_spectra.yaml

inst/params/default/create_components.yaml

inst/params/default/create_edges_spectra.yaml

inst/params/default/filter_annotations.yaml

inst/params/default/prepare_annotations_gnps.yaml

inst/params/default/prepare_annotations_sirius.yaml

inst/params/default/prepare_annotations_spectra.yaml

inst/params/default/prepare_features_components.yaml

inst/params/default/prepare_features_edges.yaml

inst/params/default/prepare_features_tables.yaml

inst/params/default/prepare_libraries_rt.yaml

inst/params/default/prepare_libraries_sop_closed.yaml

inst/params/default/prepare_libraries_sop_ecmdb.yaml

inst/params/default/prepare_libraries_sop_hmdb.yaml

inst/params/default/prepare_libraries_sop_lotus.yaml

inst/params/default/prepare_libraries_sop_merged.yaml

inst/params/default/prepare_libraries_spectra.yaml

inst/params/default/prepare_taxa.yaml

inst/params/default/weight_annotations.yaml

inst/params/prepare_params.yaml

inst/params/prepare_params_advanced.yaml

inst/paths.yaml

inst/scripts/annotate_masses.R inst/scripts/annotate_spectra.R inst/scripts/change_tests.R inst/scripts/create_components.R inst/scripts/create_edges_spectra.R inst/scripts/docopt.R

inst/scripts/docopt/annotate_masses.txt

inst/scripts/docopt/annotate_spectra.txt

inst/scripts/docopt/create_components.txt

inst/scripts/docopt/create_edges_spectra.txt

inst/scripts/docopt/filter_annotations.txt

inst/scripts/docopt/prepare_annotations_gnps.txt

inst/scripts/docopt/prepare_annotations_sirius.txt

inst/scripts/docopt/prepare_annotations_spectra.txt

inst/scripts/docopt/prepare_features_components.txt

inst/scripts/docopt/prepare_features_edges.txt

inst/scripts/docopt/prepare_features_tables.txt

inst/scripts/docopt/prepare_libraries_rt.txt

inst/scripts/docopt/prepare_libraries_sop_closed.txt

inst/scripts/docopt/prepare_libraries_sop_ecmdb.txt

inst/scripts/docopt/prepare_libraries_sop_hmdb.txt

inst/scripts/docopt/prepare_libraries_sop_lotus.txt

inst/scripts/docopt/prepare_libraries_sop_merged.txt

inst/scripts/docopt/prepare_libraries_spectra.txt

inst/scripts/docopt/prepare_params.txt

inst/scripts/docopt/prepare_taxa.txt

inst/scripts/docopt/weight_annotations.txt

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man/filter_annotations.Rd man/filter_high_confidence_only.Rd man/get_default_paths.Rd man/get_example_files.Rd man/get_example_sirius.Rd man/get_file.Rd man/get_gnps_tables.Rd man/get_last_version_from_zenodo.Rd man/get_massbank_spectra.Rd man/get_organism_taxonomy_ott.Rd man/get_params.Rd man/go_to_cache.Rd man/harmonize_adducts.Rd man/harmonize_names_sirius.Rd man/harmonize_spectra.Rd man/import_spectra.Rd man/install.Rd man/load_yaml_files.Rd man/log_debug.Rd man/log_pipe.Rd man/parse_adduct.Rd man/parse_cli_params.Rd man/parse_yaml_params.Rd man/pre_harmonize_names_sirius.Rd man/prepare_annotations_gnps.Rd man/prepare_annotations_sirius.Rd man/prepare_annotations_spectra.Rd man/prepare_features_components.Rd man/prepare_features_edges.Rd man/prepare_features_tables.Rd man/prepare_libraries_rt.Rd man/prepare_libraries_sop_closed.Rd man/prepare_libraries_sop_ecmdb.Rd man/prepare_libraries_sop_hmdb.Rd man/prepare_libraries_sop_lotus.Rd man/prepare_libraries_sop_merged.Rd man/prepare_libraries_spectra.Rd man/prepare_params.Rd man/prepare_taxa.Rd man/read_from_sirius_zip.Rd man/replace_id.Rd man/round_reals.Rd man/run_app.Rd man/sanitize_spectra.Rd man/select_annotations_columns.Rd man/select_sirius_columns_canopus.Rd man/select_sirius_columns_formulas.Rd man/select_sirius_columns_structures.Rd man/select_sop_columns.Rd man/split_tables_sop.Rd man/tima-package.Rd man/tima_full.Rd man/transform_score_sirius_csi.Rd man/weight_annotations.Rd man/weight_bio.Rd man/weight_chemo.Rd

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tests/testthat.R

tests/testthat/.gitignore

tests/testthat/_snaps/shinytest2/001.json

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tests/testthat/setup-shinytest2.R tests/testthat/test-functions.R tests/testthat/test-shinytest2.R

tima.Rproj

vignettes/.gitignore

vignettes/articles/I-gathering.Rmd vignettes/articles/II-preparing.Rmd vignettes/articles/III-processing.Rmd vignettes/articles/IV-benchmarking.Rmd

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vignettes/tima.Rmd

taxonomicallyinformedannotation/tima-r documentation built on Nov. 20, 2024, 4:34 a.m.

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taxonomicallyinformedannotation/tima-r
Taxonomically Informed Metabolite Annotation

Files in taxonomicallyinformedannotation/tima-r
Taxonomically Informed Metabolite Annotation

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taxonomicallyinformedannotation/tima-r Taxonomically Informed Metabolite Annotation

Files in taxonomicallyinformedannotation/tima-r Taxonomically Informed Metabolite Annotation

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taxonomicallyinformedannotation/tima-r
Taxonomically Informed Metabolite Annotation

Files in taxonomicallyinformedannotation/tima-r
Taxonomically Informed Metabolite Annotation