Package: omu 1.1.0

omu: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.

Authors:Connor Tiffany [aut, cre]

omu_1.1.0.tar.gz
omu_1.1.0.zip(r-4.5)omu_1.1.0.zip(r-4.4)omu_1.1.0.zip(r-4.3)
omu_1.1.0.tgz(r-4.4-any)omu_1.1.0.tgz(r-4.3-any)
omu_1.1.0.tar.gz(r-4.5-noble)omu_1.1.0.tar.gz(r-4.4-noble)
omu_1.1.0.tgz(r-4.4-emscripten)omu_1.1.0.tgz(r-4.3-emscripten)
omu.pdf |omu.html✨
omu/json (API)

# Install 'omu' in R:
install.packages('omu', repos = c('https://connor-reid-tiffany.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/connor-reid-tiffany/omu/issues

Datasets:

On CRAN:

4.87 score 3 stars 49 scripts 391 downloads 5 mentions 23 exports 112 dependencies

Last updated 1 years agofrom:556731e5f7. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winOKNov 08 2024
R-4.5-linuxOKNov 08 2024
R-4.4-winOKNov 08 2024
R-4.4-macOKNov 08 2024
R-4.3-winOKNov 08 2024
R-4.3-macOKNov 08 2024

Exports:assign_hierarchycheck_zeroscount_fold_changesget_seqsKEGG_gathermake_omeletteomu_anovaomu_summaryPCA_plotpie_chartplate_omeletteplate_omelette_rxnkoplot_barplot_boxplotplot_heatmapplot_rf_PCAplot_variable_importanceplot_volcanora_tablerandom_forestread_metabotransform_metabolitestransform_samples

Dependencies:abindaskpassbackportsbootbroomcarcarDatacaretclasscliclockcodetoolscolorspacecorrplotcowplotcpp11curldata.tableDerivdiagramdigestdoBydplyrdunn.teste1071fansifarverforeachFormulaFSAfuturefuture.applygenericsggfortifyggplot2globalsgluegowergridExtragtablehardhathttripredisobanditeratorsjsonliteKernSmoothlabelinglatticelavalifecyclelistenvlme4lmtestlubridatemagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqaModelMetricsmodelrmunsellnlmenloptrnnetnumDerivopensslparallellypbkrtestpillarpkgconfigplotrixplyrpROCprodlimprogressrproxypurrrquantregR6randomForestRColorBrewerRcppRcppEigenrecipesreshape2rlangrpartrstatixscalesshapeSparseMSQUAREMstringistringrsurvivalsystibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithrzoo

omu, a Metabolomics Analysis R Package

Connor R. Tiffany

Rendered fromOmu_vignette.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2022-04-07
Started: 2020-08-26

Readme and manuals

Help Manual

Help pageTopics
Assign hierarchy metadataassign_hierarchy
c57b6J nos2KO metabolomics count matrixc57_nos2KO_mouse_countDF
c57b6J nos2KO meta datac57_nos2KO_mouse_metadata
Check data for zeros across samples within factor levels. Will determine if there are more zeros than a user specified threshold within any given factor level(s). Returns a vector of Metabolites that are 0 above the threshold in any given factor level.check_zeros
Get counts for significant fold changes by metabolite class.count_fold_changes
Get nucleotide and amino acid sequences for genesget_seqs
Gather metadata from KEGG for metabolitesKEGG_gather KEGG_gather.cpd KEGG_gather.KO KEGG_gather.rxn
Get metadata from KEGG APImake_omelette
Perform anovaomu_anova
omu_summary Performs comparison of means between two independent variables, standard deviation, standard error, FDR correction, fold change, log2FoldChange. The order effects the fold change valuesomu_summary
Create a PCA plotPCA_plot
Create a pie chartpie_chart
plate_omelette Internal method for KEGG_Gather which parses flat text filesplate_omelette plate_omelette.genes plate_omelette.KO plate_omelette.rxn
Clean up orthology metadataplate_omelette_rxnko
Create a bar plotplot_bar
Create a box plotplot_boxplot
Create a heatmapplot_heatmap
plot_rf_PCAplot_rf_PCA
plot_variable_importanceplot_variable_importance
Create a volcano plotplot_volcano
Creates a ratio table from the count_fold_changes function output.ra_table
random_forest Perform a classification or regression random forest modelrandom_forest
Import a metabolomics count data frameread_metabo
transform_metabolitestransform_metabolites
transform_samplestransform_samples