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 External 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 | Which version is installed and loaded? | What is new? | 7. UME installation
Package: ume 1.6.1
Boris Koch
ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter
Provides tools for assigning molecular formulas from exact masses obtained by ultrahigh-resolution mass spectrometry. The methodology follows the workflow described in Leefmann et al. (2019) <doi:10.1002/rcm.8315>. The package supports the inspection, filtering and visualization of molecular formula data and includes utilities for calculating common molecular parameters (e.g., double bond equivalents, DBE). A graphical user interface is available via the 'shiny'-based 'ume' application.
Authors:
ume_1.6.1.tar.gz
ume_1.6.1.tar.gz(r-4.7-any)ume_1.6.1.tar.gz(r-4.6-any)
ume_1.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ume/json (API)
| # Install 'ume' in R: |
| install.packages('ume', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- known_mf - Collection of known formulas, for which additional information is available.
- lib_demo - Demo formula library
- masses - Masses: Elements and isotopes
- mf_data_demo - Mf_data_demo
- nice_labels_dt - Nice_labels_dt
- peaklist_demo - Demo peak list
- tab_ume_labels - Labels of UME columns.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:4adb3eb2ff. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 198 | ||
| source / vignettes | OK | 293 | ||
| linux-release-x86_64 | OK | 195 | ||
| wasm-release | OK | 142 |
Exports:add_known_mfadd_missing_element_columnsas_peaklistassign_formulascalc_data_summarycalc_dbecalc_eval_paramscalc_exact_masscalc_idegcalc_isotope_patterncalc_iterrcalc_macalc_ma_abscalc_neutral_masscalc_nmcalc_norm_intcalc_number_assignmentcalc_pielou_evennesscalc_recalibrate_mscalc_shannon_indexcalc_simpson_indexcheck_neutral_mfclassify_filescolor.paletteconvert_data_table_to_molecular_formulasconvert_molecular_formula_to_data_tablecreate_custom_formula_librarycreate_isotope_expanded_tablecreate_ume_formula_librarydownload_libraryeval_isotopesfilter_intfilter_mass_accuracyfilter_mf_dataget_isotope_infoinchi_to_mfis_ume_peaklistorder_columnsremove_blanksremove_empty_columnssubset_known_mftheme_uplotsume_assign_formulasume_filter_formulasuplot_clusteruplot_cvmuplot_dbe_minus_o_frequplot_dbe_vs_cuplot_dbe_vs_mauplot_frequplot_freq_mauplot_freq_vs_ppmuplot_hc_vs_muplot_heteroatomsuplot_isotope_precisionuplot_kmduplot_lcmsuplot_ma_vs_mzuplot_msuplot_n_mf_per_sampleuplot_pcauplot_ratiosuplot_reproducibilityuplot_ri_vs_sampleuplot_vkustats_outlier
Dependencies:askpassbase64encbslibcachemcliclustercpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimenlmeopensslotelpermutepillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsveganviridisviridisLitewithrxfunyaml
