{ "_id": "6a5758feff0138dec5d70b6d", "Package": "ume", "Title": "Ultrahigh-Resolution Mass Spectrometry Data Evaluation for\nComplex Organic Matter", "Version": "1.7.1", "Authors@R": "c(\nperson(\"Boris\", \"Koch\",\nemail = \"boris.koch@awi.de\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8453-731X\")),\nperson(\"Stephan\", \"Frickenhaus\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-0356-9791\")),\nperson(\"Shuxian\", \"Gao\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0009-0004-7819-7525\")),\nperson(\"Oliver\", \"Lechtenfeld\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-5313-6014\")),\nperson(\"Tim\", \"Leefmann\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-5784-8657\")),\nperson(\"Fabian\", \"Moye\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4632-5033\"))\n)", "Description": "Provides tools for assigning molecular formulas from exact\nmasses obtained by ultrahigh-resolution mass spectrometry. The\nmethodology follows the workflow described in Leefmann et al.\n(2019) . The package supports the\ninspection, filtering and visualization of molecular formula\ndata and includes utilities for calculating common molecular\nparameters (e.g., double bond equivalents, DBE). A graphical\nuser interface is available via the 'shiny'-based 'ume'\napplication.", "URL": "https://gitlab.awi.de/bkoch/ume, https://github.com/boriskoch/ume,\nhttps://doi.org/10.5281/zenodo.20108477,\nhttps://www.awi.de/en/ume", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "RoxygenNote": "8.0.0", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev", "Repository": "https://boriskoch.r-universe.dev", "Date/Publication": "2026-07-13 20:38:37 UTC", "RemoteUrl": "https://github.com/boriskoch/ume", "RemoteRef": "HEAD", "RemoteSha": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-15 09:49:39 UTC", "User": "root" }, "Author": "Boris Koch [aut, cre] (ORCID: ),\nStephan Frickenhaus [ctb] (ORCID:\n),\nShuxian Gao [ctb] (ORCID: ),\nOliver Lechtenfeld [ctb] (ORCID:\n),\nTim Leefmann [ctb] (ORCID: ),\nFabian Moye [ctb] (ORCID: )", "Maintainer": "Boris Koch ", "_user": "boriskoch", "_type": "src", "_file": "ume_1.7.1.tar.gz", "_fileid": "https://r2.ropensci.org/511d6280456fd2d750175e0712336695fdea1e5e9a8fa255fa8c0f0764d99d4b", "_filesize": 3890380, "_sha256": "511d6280456fd2d750175e0712336695fdea1e5e9a8fa255fa8c0f0764d99d4b", "_expires": "2026-10-23T09:55:07.000Z", "_created": "2026-07-15T09:49:39.000Z", "_published": "2026-07-15T09:55:10.513Z", "_jobs": [ { "job": 87321439514, "time": 247, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8339144658" }, { "job": 87321439516, "time": 188, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8339122062" }, { "job": 87321439562, "time": 207, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8339116511" }, { "job": 87321439547, "time": 201, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8339113944" }, { "job": 87320387319, "time": 311, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8339045470" }, { "job": 87321439537, "time": 147, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8339105814" }, { "job": 87321439561, "time": 195, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8339124873" }, { "job": 87321439622, "time": 159, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8339111063" }, { "job": 87321439625, "time": 160, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8339110921" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306", "_status": "success", "_upstream": "https://github.com/boriskoch/ume", "_commit": { "id": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "author": "Boris Peter Koch ", "committer": "Boris Peter Koch ", "message": "Prepare UME 1.7.1 CRAN candidate\n", "time": 1783975117 }, "_maintainer": { "name": "Boris Koch", "email": "boris.koch@awi.de", "orcid": "0000-0002-8453-731X" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.5.0", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" }, { "package": "pdftools", "role": "Suggests" }, { "package": "KEGGREST", "role": "Suggests" }, { "package": "zCompositions", "role": "Suggests" } ], "_owner": "boriskoch", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-19", "n": 5 }, { "week": "2026-28", "n": 7 }, { "week": "2026-29", "n": 2 } ], "_tags": [ { "name": "v1.6.1", "date": "2026-05-09" }, { "name": "v1.6.1a", "date": "2026-05-10" }, { "name": "v1.6.1b", "date": "2026-05-10" } ], "_stars": 0, "_contributors": [ { "user": "boriskoch", "count": 13, "uuid": 61932683 } ], "_userbio": { "uuid": 61932683, "type": "user", "name": "boriskoch", "followers": 0 }, "_downloads": { "count": 361, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ume" }, "_devurl": "https://github.com/boriskoch/ume", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/ume.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/boriskoch/ume", "_realowner": "boriskoch", "_cranurl": true, "_releases": [ { "version": "1.5.2", "date": "2025-12-12" }, { "version": "1.6.1", "date": "2026-05-09" }, { "version": "1.7.1", "date": "2026-07-14" } ], "_exports": [ "add_known_mf", "add_missing_element_columns", "as_mfd", "as_peaklist", "as_ume_matrix", "assign_formulas", "calc_data_summary", "calc_dbe", "calc_eval_params", "calc_exact_mass", "calc_ideg", "calc_isotope_pattern", "calc_iterr", "calc_logratio", "calc_ma", "calc_ma_abs", "calc_neutral_mass", "calc_nm", "calc_norm_int", "calc_number_assignment", "calc_pielou_evenness", "calc_recalibrate_ms", "calc_shannon_index", "calc_simpson_index", "check_neutral_mf", "classify_files", "color.palette", "convert_data_table_to_molecular_formulas", "convert_molecular_formula_to_data_table", "create_custom_formula_library", "create_isotope_expanded_table", "create_time_flattened_mfd", "create_ume_formula_library", "download_library", "eval_isotopes", "filter_int", "filter_mass_accuracy", "filter_mf_data", "filter_multi_assignments", "get_isotope_info", "inchi_to_mf", "is_ume_peaklist", "order_columns", "remove_blanks", "remove_empty_columns", "subset_known_mf", "theme_uplots", "ume_assign_formulas", "ume_filter_formulas", "uplot_cluster", "uplot_cvm", "uplot_dbe_minus_o_freq", "uplot_dbe_vs_c", "uplot_dbe_vs_ma", "uplot_freq", "uplot_freq_ma", "uplot_freq_vs_ppm", "uplot_hc_vs_m", "uplot_heteroatoms", "uplot_isotope_precision", "uplot_kmd", "uplot_lcms", "uplot_ma_vs_mz", "uplot_ms", "uplot_n_mf_per_sample", "uplot_pca", "uplot_ratios", "uplot_reproducibility", "uplot_ri_vs_sample", "uplot_vk", "ustats_outlier", "zero_filling" ], "_datasets": [ { "name": "known_mf", "title": "Collection of known formulas, for which additional information is available.", "object": "known_mf", "class": [ "data.table", "data.frame" ], "fields": [ "mf_kf_id", "mf", "category", "info1", "info2", "info3", "info4", "reference", "mass" ], "rows": 302476, "table": true, "tojson": true }, { "name": "lib_demo", "title": "Demo formula library (200 - 300 Da, neutral mass)", "object": "lib_demo", "class": [ "data.table", "data.frame" ], "fields": [ "vkey", "mf", "mass", "12C", "13C", "1H", "14N", "15N", "16O", "31P", "32S", "34S" ], "rows": 115111, "table": true, "tojson": true }, { "name": "masses", "title": "Masses: Elements and isotopes", "object": "masses", "class": [ "data.table", "data.frame" ], "fields": [ "label", "symbol", "nm", "exact_mass", "mole_fraction", "relative_abundance", "valence", "valence2", "hill_order" ], "rows": 288, "table": true, "tojson": true }, { "name": "mf_data_demo", "title": "mf_data_demo", "object": "mf_data_demo", "class": [ "data.table", "data.frame" ], "fields": [ "file_id", "file", "peak_id", "mz", "i_magnitude", "norm_int", "m", "m_cal", "ppm", "nm", "mf", "dbe", "12C", "1H", "14N", "16O", "31P", "32S", "hc", "oc", "nc", "sc", "ai", "z", "kmd", "ppm_filt", "mf_id", "int15n", "int34s", "int13c", "s_n", "res", "del", "dev_n_c", "dbe_o", "nosc", "delg0_cox", "relint13c_calc", "int13c_calc", "relint34s_calc", "int34s_calc", "snp_check", "nsp_type", "co_tot", "nsp_tot", "n_occurrence_orig", "n_assignments_orig", "int_bp", "n_assignments", "int_ref" ], "rows": 9245, "table": true, "tojson": true }, { "name": "peaklist_demo", "title": "Demo peak list", "object": "peaklist_demo", "class": [ "data.table", "data.frame" ], "fields": [ "file_id", "file", "peak_id", "mz", "i_magnitude", "s_n", "res" ], "rows": 31091, "table": true, "tojson": true }, { "name": "ume_logo_raster", "title": "Internal raster of the UME logo", "object": "ume_logo_raster", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "ume_name_dictionary", "title": "UME name dictionary", "object": "ume_name_dictionary", "class": [ "data.table", "data.frame" ], "fields": [ "source_system", "source_name", "label", "synonym_name", "nice_label", "semantic_type", "target", "priority", "unit" ], "rows": 60, "table": true, "tojson": true } ], "_help": [ { "page": "add_known_mf", "title": "Add metainformation derived from ume::known_mf", "concept": [ "Formula assignment" ], "topics": [ "add_known_mf" ] }, { "page": "add_missing_element_columns", "title": "Add Missing Isotope Columns to mfd", "concept": [ "tools" ], "topics": [ "add_missing_element_columns" ] }, { "page": "as_mfd", "title": "Coerce input to UME molecular formula data", "concept": [ "check ume objects" ], "topics": [ "as_mfd" ] }, { "page": "as_peaklist", "title": "Check format of peaklist", "concept": [ "check ume objects" ], "topics": [ "as_peaklist" ] }, { "page": "as_ume_matrix", "title": "Convert molecular formula data to a feature matrix", "topics": [ "as_ume_matrix" ] }, { "page": "assign_formulas", "title": "Molecular Formula Assignment", "topics": [ "assign_formulas" ] }, { "page": "calc_data_summary", "title": "Create a Data Summary Table for Element Ratios and Parameters", "concept": [ "calculations" ], "topics": [ "calc_data_summary" ] }, { "page": "calc_dbe", "title": "Calculate Double Bond Equivalent (DBE)", "concept": [ "calculations" ], "topics": [ "calc_dbe" ] }, { "page": "calc_eval_params", "title": "Calculate UME Evaluation Parameters", "concept": [ "Formula assignment", "calculations" ], "topics": [ "calc_eval_params" ] }, { "page": "calc_exact_mass", "title": "Calculate Exact Monoisotopic Mass of a Molecule", "concept": [ "calculations" ], "topics": [ "calc_exact_mass" ] }, { "page": "calc_ideg", "title": "Calculate Degradation Index (Ideg)", "concept": [ "calculations" ], "topics": [ "calc_ideg" ] }, { "page": "calc_isotope_pattern", "title": "Calculate Isotope Pattern", "concept": [ "isotopes" ], "topics": [ "calc_isotope_pattern" ] }, { "page": "calc_iterr", "title": "Calculate terrestrial indeces Iterr and Iterr2 (after Medeiros et al. 2016)", "concept": [ "index calculations" ], "topics": [ "calc_iterr" ] }, { "page": "calc_logratio", "title": "calc_logratio", "topics": [ "calc_logratio" ] }, { "page": "calc_ma", "title": "Calculate mass accuracy", "concept": [ "calculations" ], "topics": [ "calc_ma" ] }, { "page": "calc_ma_abs", "title": "Calculate absolute mass accuracy range (ma)", "topics": [ "calc_ma_abs" ] }, { "page": "calc_neutral_mass", "title": "Calculate neutral molecular mass", "concept": [ "calculations" ], "topics": [ "calc_neutral_mass" ] }, { "page": "calc_nm", "title": "Calculate Nominal Mass of a Molecule", "concept": [ "calculations" ], "topics": [ "calc_nm" ] }, { "page": "calc_norm_int", "title": "Calculate Normalized Peak Intensities", "concept": [ "calculations" ], "topics": [ "calc_norm_int" ] }, { "page": "calc_number_assignment", "title": "Calculate Number of Molecular Formula Assignments per Peak", "concept": [ "calculations" ], "topics": [ "calc_number_assignment" ] }, { "page": "calc_pielou_evenness", "title": "Calculate Pielou's Evenness", "topics": [ "calc_pielou_evenness" ] }, { "page": "calc_shannon_index", "title": "Calculate the Shannon Diversity Index", "topics": [ "calc_shannon_index" ] }, { "page": "calc_simpson_index", "title": "Calculate the Simpson Diversity Index", "topics": [ "calc_simpson_index" ] }, { "page": "calc_time_flattened_mfd", "title": "Create a time-flattened molecular formula data table", "topics": [ "calc_time_flattened_mfd", "create_time_flattened_mfd" ] }, { "page": "check_neutral_mf", "title": "Check neutral molecular formulas", "concept": [ "molecular formula functions" ], "topics": [ "check_neutral_mf" ] }, { "page": "classify_files", "title": "Classify FTMS files into categories based on filename patterns", "concept": [ "helper" ], "topics": [ "classify_files" ] }, { "page": "color.palette", "title": "Create a Custom Interpolated Color Palette", "topics": [ "color.palette" ] }, { "page": "convert_data_table_to_molecular_formulas", "title": "Convert Data Table with Element Counts to Molecular Formulas", "concept": [ "molecular formula functions" ], "topics": [ "convert_data_table_to_molecular_formulas" ] }, { "page": "convert_molecular_formula_to_data_table", "title": "Convert Molecular Formulas to a Data Table of Element Counts", "concept": [ "molecular formula functions" ], "topics": [ "convert_molecular_formula_to_data_table" ] }, { "page": "create_isotope_expanded_table", "title": "Create an Expanded Table of Parent and Isotope Daughter Formulas", "concept": [ "isotopes" ], "topics": [ "create_isotope_expanded_table" ] }, { "page": "create_ume_formula_library", "title": "Create a molecular formula library for UME", "topics": [ "create_ume_formula_library" ] }, { "page": "download_library", "title": "Download and Load a UME Formula Library", "topics": [ "download_library" ] }, { "page": "eval_isotopes", "title": "Evaluate isotope information", "concept": [ "Formula assignment", "isotopes" ], "topics": [ "eval_isotopes" ] }, { "page": "filter_int", "title": "Filter by (relative) peak magnitude", "concept": [ "Formula subsetting" ], "topics": [ "filter_int" ] }, { "page": "filter_mass_accuracy", "title": "Automated filter for mass accuracy", "concept": [ "Formula subsetting" ], "topics": [ "filter_mass_accuracy" ] }, { "page": "filter_mf_data", "title": "Filter molecular formula data by mass spectrometric metadata", "concept": [ "Formula subsetting" ], "topics": [ "filter_mf_data" ] }, { "page": "filter_multi_assignments", "title": "Filter multiple molecular formula assignments by mass-error medians", "topics": [ "filter_multi_assignments" ] }, { "page": "get_isotope_info", "title": "Retrieve NIST element and isotope data", "topics": [ "get_isotope_info" ] }, { "page": "inchi_to_mf", "title": "Extract molecular formula from InChI string", "topics": [ "inchi_to_mf" ] }, { "page": "is_ume_peaklist", "title": "Check whether an object is a UME peaklist", "topics": [ "is_ume_peaklist" ] }, { "page": "known_mf", "title": "Collection of known formulas, for which additional information is available.", "concept": [ "ume data" ], "topics": [ "known_mf" ] }, { "page": "lib_demo", "title": "Demo formula library (200 - 300 Da, neutral mass)", "concept": [ "ume data" ], "topics": [ "lib_demo" ] }, { "page": "masses", "title": "Masses: Elements and isotopes", "concept": [ "ume data" ], "topics": [ "masses" ] }, { "page": "mf_data_demo", "title": "mf_data_demo", "concept": [ "ume data" ], "topics": [ "mf_data_demo" ] }, { "page": "order_columns", "title": "Order columns", "concept": [ "tools" ], "topics": [ "order_columns" ] }, { "page": "peaklist_demo", "title": "Demo peak list", "concept": [ "ume data" ], "topics": [ "peaklist_demo" ] }, { "page": "remove_blanks", "title": "Remove molecular formulas detected in blanks", "concept": [ "Formula subsetting" ], "topics": [ "remove_blanks" ] }, { "page": "remove_empty_columns", "title": "Remove empty columns", "topics": [ "remove_empty_columns" ] }, { "page": "remove_id_columns", "title": "Remove columns that contain ID's", "concept": [ "Clean data output" ], "topics": [ "remove_id_columns" ] }, { "page": "remove_unknown_columns", "title": "Remove columns that only have one specific value", "concept": [ "Clean data output" ], "topics": [ "remove_unknown_columns" ] }, { "page": "subset_known_mf", "title": "Subsetting known molecular formula categories", "concept": [ "Formula subsetting" ], "topics": [ "subset_known_mf" ] }, { "page": "theme_uplots", "title": "theme_uplots", "topics": [ "theme_uplots" ] }, { "page": "ume_assign_formulas", "title": "Complete formula assignment (wrapper function)", "concept": [ "Formula assignment", "Formula subsetting", "ume wrapper" ], "topics": [ "ume_assign_formulas" ] }, { "page": "ume_filter_formulas", "title": "Complete Formula subsetting / filtering (wrapper)", "concept": [ "Formula subsetting", "ume wrapper" ], "topics": [ "ume_filter_formulas" ] }, { "page": "ume_name_dictionary", "title": "UME name dictionary", "concept": [ "ume data" ], "topics": [ "ume_name_dictionary" ] }, { "page": "uplot_cluster", "title": "uplot_cluster", "concept": [ "uplots" ], "topics": [ "uplot_cluster" ] }, { "page": "uplot_cvm", "title": "Carbon vs Mass (CvM) Diagram", "concept": [ "uplots" ], "topics": [ "uplot_cvm" ] }, { "page": "uplot_dbe_minus_o_freq", "title": "Frequency Plot of DBE - O atoms", "concept": [ "uplots" ], "topics": [ "uplot_dbe_minus_o_freq" ] }, { "page": "uplot_dbe_vs_c", "title": "Plot DBE vs Carbon Atoms", "concept": [ "uplots" ], "topics": [ "uplot_dbe_vs_c" ] }, { "page": "uplot_dbe_vs_ma", "title": "Plot DBE vs ppm with Option for Interactive Plot", "concept": [ "uplots" ], "topics": [ "uplot_dbe_vs_ma" ] }, { "page": "uplot_dbe_vs_o", "title": "Plot DBE vs Oxygen Atoms (cf. Herzsprung et al. 2014) with Option for Interactive Plot", "concept": [ "uplots" ], "topics": [ "uplot_dbe_vs_o" ] }, { "page": "uplot_freq", "title": "Frequency Plot of a Selected Variable", "topics": [ "uplot_freq" ] }, { "page": "uplot_freq_ma", "title": "Histogram of Mass Accuracy", "concept": [ "uplots" ], "topics": [ "uplot_freq_ma" ] }, { "page": "uplot_freq_vs_ppm", "title": "Mass Accuracy Frequency Histogram", "concept": [ "uplots" ], "topics": [ "uplot_freq_vs_ppm" ] }, { "page": "uplot_hc_vs_m", "title": "H/C vs Molecular Mass Plot", "concept": [ "uplots" ], "topics": [ "uplot_hc_vs_m" ] }, { "page": "uplot_heteroatoms", "title": "Heteroatom Combination vs Mass Accuracy", "concept": [ "uplots" ], "topics": [ "uplot_heteroatoms" ] }, { "page": "uplot_isotope_precision", "title": "Precision of Isotope Abundance", "concept": [ "isotopes", "uplots" ], "topics": [ "uplot_isotope_precision" ] }, { "page": "uplot_kmd", "title": "Kendrick Mass Defect (KMD) vs. Nominal Mass Plot", "concept": [ "uplots" ], "topics": [ "uplot_kmd" ] }, { "page": "uplot_lcms", "title": "Plot LC-MS Spectrum (or fallback MS if no RT available)", "concept": [ "uplots" ], "topics": [ "uplot_lcms" ] }, { "page": "uplot_ma_vs_mz", "title": "Plot Mass Accuracy vs m/z", "concept": [ "uplots" ], "topics": [ "uplot_ma_vs_mz" ] }, { "page": "uplot_ms", "title": "Plot Mass Spectrum", "concept": [ "uplots" ], "topics": [ "uplot_ms" ] }, { "page": "uplot_n_mf_per_sample", "title": "Number of Molecular Formulas per Sample Plot", "concept": [ "uplots" ], "topics": [ "uplot_n_mf_per_sample" ] }, { "page": "uplot_pca", "title": "Plot PCA Results", "concept": [ "uplots" ], "topics": [ "uplot_pca" ] }, { "page": "uplot_ppm_avg", "title": "Plot Median of Mass Accuracy per Sample (ppm)", "topics": [ "uplot_ppm_avg" ] }, { "page": "uplot_ratios", "title": "Molecular Formula Ratio Plot (Sample vs Control)", "concept": [ "uplots" ], "topics": [ "uplot_ratios" ] }, { "page": "uplot_reproducibility", "title": "Check Reproducibility of Sample Analyses", "concept": [ "uplots" ], "topics": [ "uplot_reproducibility" ] }, { "page": "uplot_ri_vs_sample", "title": "Median Relative Intensity per Sample", "concept": [ "uplots" ], "topics": [ "uplot_ri_vs_sample" ] }, { "page": "uplot_vk", "title": "uplot_vk", "concept": [ "uplots" ], "topics": [ "uplot_vk" ] }, { "page": "ustats_outlier", "title": "Outlier detection using multiple statistical tests", "topics": [ "ustats_outlier" ] }, { "page": "zero_filling", "title": "zero_filling", "topics": [ "zero_filling" ] } ], "_pkglogo": "https://github.com/boriskoch/ume/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/boriskoch/ume/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bslib", "cachem", "cli", "cluster", "cpp11", "crosstalk", "curl", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mgcv", "mime", "nlme", "openssl", "otel", "permute", "pillar", "pkgconfig", "plotly", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "vegan", "viridis", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "ume.Rmd", "filename": "ume.html", "title": "ume", "author": "Boris Koch", "engine": "knitr::rmarkdown", "headings": [ "Getting started", "1. Overview UME data workflow", "All of these tasks can be executed in just two steps:", "Formula assignment and calculation of evaluation parameters", "Formula filtering (subsetting) and normalization", "Alternatively, the workflow can be performed in single steps:", "2. Visualization and statistics", "3. Re-calibration of peaklists", "4. UME core data objects", "Mass Peak List", "Isotopic masses", "Molecular formula library", "Using Pre-defined UME Formula Libraries", "Create your own molecular formula library", "Molecular formula data", "5. What else can you do with ume?", "Calculate standard parameters", "Converting molecular formulas to a table and vice versa.", "Isotopes", "Create isotope formulas for a parent formula", "Create isotope pattern for a molecular formula", "6. Package content and documentation", "Github for public releases of R code", "All package versions on Zenodo", "Which version is installed and loaded?", "What is new?", "Complete manual", "7. UME installation", "8. UME shiny app" ], "created": "2026-05-09 20:24:19", "modified": "2026-07-13 20:38:37", "commits": 3 } ], "_score": 4.176091259055681, "_indexed": true, "_nocasepkg": "ume", "_universes": [ "boriskoch" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.1", "date": "2026-07-15T09:53:03.000Z", "distro": "resolute", "commit": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "fileid": "https://r2.ropensci.org/d5086867f3a1171584d0581a93f2ca3843d5918c93846c0ce87887ce3b13896c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306" }, { "r": "4.6.1", "os": "linux", "version": "1.7.1", "date": "2026-07-15T09:52:40.000Z", "distro": "resolute", "commit": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "fileid": "https://r2.ropensci.org/8353a37096917a676b3c8e50b45bbf1ee7d969568c7ee869b953d863b0c80a55", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306" }, { "r": "4.5.3", "os": "mac", "version": "1.7.1", "date": "2026-07-15T09:52:21.000Z", "commit": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "fileid": "https://r2.ropensci.org/ba9e250c3b26bb53c9bc558251e3655452dd34da0aa7d166cc29edf4329202ce", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306" }, { "r": "4.6.1", "os": "mac", "version": "1.7.1", "date": "2026-07-15T09:52:11.000Z", "commit": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "fileid": "https://r2.ropensci.org/c8d94fe3a6d2de95e44806dfeb7d0d71def7415c0fbbb072241aa03dd50c1273", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.1", "date": "2026-07-15T09:52:46.000Z", "commit": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "fileid": "https://r2.ropensci.org/9447905b859cf112aea112d7653c172958c4bf83b8dbba1341d11cd19ea7fddc", "status": "success", "buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306" }, { "r": "4.7.0", "os": "win", "version": "1.7.1", "date": "2026-07-15T09:52:03.000Z", "commit": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "fileid": "https://r2.ropensci.org/c020904767427e44086f6006a839eb76e37e5ac412f54160f255e7b4a376bb4c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306" }, { "r": "4.5.3", "os": "win", "version": "1.7.1", "date": "2026-07-15T09:51:25.000Z", "commit": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "fileid": "https://r2.ropensci.org/9becca04ffa2f197b400a06e5d91562303a83eaab0f45eb947e92fda8a56fd3e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306" }, { "r": "4.6.1", "os": "win", "version": "1.7.1", "date": "2026-07-15T09:51:25.000Z", "commit": "e59b8eb447e140c8c3c4e4349eace4786fe380b0", "fileid": "https://r2.ropensci.org/75182f3006bc82ae99c28fa938de4479460e19186eac4323e3363b671d24b898", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/boriskoch/actions/runs/29405648306" } ] }