Files in taxonomicallyinformedannotation/tima-r
Taxonomically Informed Metabolite Annotation

.Rbuildignore
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.github/.gitignore
.github/CODE_OF_CONDUCT.md .github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/custom.md .github/ISSUE_TEMPLATE/feature_request.md .github/ISSUE_TEMPLATE/issue_template.md .github/PULL_REQUEST_TEMPLATE/pull_request_template.md .github/SECURITY.md .github/SUPPORT.md
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.github/workflows/test-coverage.yaml
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.gitignore
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_score.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
inst/scripts/filter_annotations.R inst/scripts/get_benchmark.R inst/scripts/get_ecmdb.R inst/scripts/get_example_features.R inst/scripts/get_example_metadata.R inst/scripts/get_example_sirius.R inst/scripts/get_example_spectra.R inst/scripts/get_gnps_tables.R inst/scripts/get_hmdb.R inst/scripts/get_isdb_hmdb.R inst/scripts/get_isdb_lotus.R inst/scripts/get_lotus.R inst/scripts/get_massbank_spectra.R inst/scripts/prepare_annotations_gnps.R inst/scripts/prepare_annotations_sirius.R inst/scripts/prepare_annotations_spectra.R inst/scripts/prepare_features_components.R inst/scripts/prepare_features_edges.R inst/scripts/prepare_features_tables.R inst/scripts/prepare_libraries_rt.R inst/scripts/prepare_libraries_sop_closed.R inst/scripts/prepare_libraries_sop_ecmdb.R inst/scripts/prepare_libraries_sop_hmdb.R inst/scripts/prepare_libraries_sop_lotus.R inst/scripts/prepare_libraries_sop_merged.R inst/scripts/prepare_libraries_spectra.R inst/scripts/prepare_libraries_spectra_is_lotus.R inst/scripts/prepare_params.R inst/scripts/prepare_taxa.R inst/scripts/tima_full.R inst/scripts/weight_annotations.R man/annotate_masses.Rd man/annotate_spectra.Rd man/benchmark_taxize_spectra.Rd man/calculate_entropy_score.Rd man/calculate_mass_of_m.Rd man/change_params_small.Rd man/clean_bio.Rd man/clean_chemo.Rd man/clean_collapse.Rd man/columns_model.Rd man/complement_metadata_structures.Rd man/copy_backbone.Rd man/create_components.Rd man/create_dir.Rd man/create_edges.Rd man/create_edges_spectra.Rd man/decorate_bio.Rd man/decorate_chemo.Rd man/decorate_masses.Rd man/dist_get.Rd man/dist_groups.Rd man/export_output.Rd man/export_params.Rd man/export_spectra_rds.Rd man/extract_spectra.Rd man/fake_annotations_columns.Rd man/fake_ecmdb.Rd man/fake_hmdb.Rd man/fake_lotus.Rd man/fake_sop_columns.Rd
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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
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tests/testthat/setup-shinytest2.R tests/testthat/test-functions.R tests/testthat/test-shinytest2.R
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 Dec. 20, 2024, 9:32 a.m.