Files in taxonomicallyinformedannotation/tima-r

Taxonomically Informed Metabolite Annotation

.Rbuildignore

.dockerignore

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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/linters/.mega-linter.yml

.github/renovate.json

.github/workflows/archive-github-pages.yml

.github/workflows/check-standard.yaml

.github/workflows/clear-cache.yml

.github/workflows/docker.yml

.github/workflows/external-use.yaml

.github/workflows/mega-linter.yml

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.github/workflows/remove-old-artifacts.yml

.github/workflows/test-coverage.yaml

.gitignore

CITATION.cff

DESCRIPTION

Dockerfile

LICENSE.md

NAMESPACE

NEWS.md R/annotate_masses.R R/annotate_spectra.R R/calculate_entropy.R R/clean_bio.R R/clean_chemo.R R/clean_collapse.R R/columns_model.R R/complement_metadata_structures.R R/create_adducts.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.R R/export_spectra_2.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_nitrogen_rule.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/harmonize_names_sirius.R R/harmonize_spectra.R R/import_spectra.R R/install_latest_version.R R/keep_peaks.R R/load_yaml_files.R R/log_debug.R R/log_pipe.R R/normalize_peaks.R R/parse_cli_params.R R/parse_yaml_params.R R/parse_yaml_paths.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_adducts.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/remove_above_precursor.R R/replace_id.R R/round_reals.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/taxize_spectra_benchmark.R R/weight_annotations.R R/weight_bio.R R/weight_chemo.R README.md

_pkgdown.yml

_targets.yaml

codecov.yml

codemeta.json

cran-comments.md

data/.gitignore

docker-compose.yml

inst/CITATION

inst/WORDLIST

inst/app.R

inst/extdata/adducts.tsv

inst/extdata/clusters.tsv

inst/extdata/neutral_losses.tsv

inst/extdata/paths.yaml

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_adducts.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/pipelines/_targets.R 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_adducts.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/install.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_adducts.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_exp_mona.R inst/scripts/prepare_libraries_spectra_is_hmdb.R inst/scripts/prepare_libraries_spectra_is_lotus.R inst/scripts/prepare_params.R inst/scripts/prepare_taxa.R inst/scripts/run_app.R inst/scripts/standardize.R inst/scripts/tima_full.R inst/scripts/weight_annotations.R man/annotate_masses.Rd man/annotate_spectra.Rd man/calculate_entropy.Rd man/clean_bio.Rd man/clean_chemo.Rd man/clean_collapse.Rd man/columns_model.Rd man/complement_metadata_structures.Rd man/create_adducts.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.Rd man/export_spectra_2.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_nitrogen_rule.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/harmonize_names_sirius.Rd man/harmonize_spectra.Rd man/import_spectra.Rd man/install_latest_version.Rd man/keep_peaks.Rd man/load_yaml_files.Rd man/log_debug.Rd man/log_pipe.Rd man/normalize_peaks.Rd man/parse_cli_params.Rd man/parse_yaml_params.Rd man/parse_yaml_paths.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_adducts.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/remove_above_precursor.Rd man/replace_id.Rd man/round_reals.Rd man/sanitize_spectra.Rd man/select_annotations_columns.Rd man/select_sirius_columns.Rd man/select_sirius_columns_2.Rd man/select_sop_columns.Rd man/split_tables_sop.Rd man/taxize_spectra_benchmark.Rd man/weight_annotations.Rd man/weight_bio.Rd man/weight_chemo.Rd

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tests/spelling.R 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

timaR.Rproj

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

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vignettes/timaR.Rmd

taxonomicallyinformedannotation/tima-r documentation built on May 17, 2024, 6:30 a.m.