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]

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omu_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
omu/json (API)

# Install 'omu' in R:

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

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

Datasets:

c57_nos2KO_mouse_countDF - C57b6J nos2KO metabolomics count matrix
c57_nos2KO_mouse_metadata - C57b6J nos2KO meta data

On CRAN:

4.95 score 3 stars 59 scripts 320 downloads 5 mentions 23 exports 132 dependencies

Last updated from:556731e5f7. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	206
source / vignettes	OK	286
linux-release-x86_64	OK	246
macos-release-arm64	OK	263
macos-oldrel-arm64	OK	231
windows-devel	OK	155
windows-release	OK	142
windows-oldrel	OK	143
wasm-release	OK	158

Exports:assign_hierarchy check_zeros count_fold_changes get_seqs KEGG_gather make_omelette omu_anova omu_summary PCA_plot pie_chart plate_omelette plate_omelette_rxnko plot_bar plot_boxplot plot_heatmap plot_rf_PCA plot_variable_importance plot_volcano ra_table random_forest read_metabo transform_metabolites transform_samples

Dependencies:abind askpass backports boot broom ca car carData caret class cli clock cluster codetools colorspace corrplot corrr cowplot cpp11 curl data.table Deriv diagram digest doBy dplyr dunn.test e1071 farver FlexParamCurve foreach forecast Formula fracdiff FSA future future.apply gclus generics ggfortify ggplot2 ggrepel globals glue gower gridExtra gtable hardhat httr ipred isoband iterators jsonlite KernSmooth labeling lattice lava lifecycle listenv lme4 lmtest lubridate magrittr MASS Matrix MatrixModels mgcv microbenchmark mime minqa ModelMetrics modelr nlme nloptr nnet numDeriv openssl parallelly pbkrtest permute pillar pkgconfig plotrix plyr pROC prodlim progressr proxy purrr qap quantreg R6 randomForest rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack recipes reformulas registry reshape2 rlang rpart rstatix S7 scales scrutiny seriation shape SparseM sparsevctrs SQUAREM stringi stringr survival sys tibble tidyr tidyselect timechange timeDate TSP tzdb urca utf8 vctrs vegan viridisLite withr zoo

omu, a Metabolomics Analysis R Package

Rendered fromOmu_vignette.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Assign hierarchy metadata	assign_hierarchy
c57b6J nos2KO metabolomics count matrix	c57_nos2KO_mouse_countDF
c57b6J nos2KO meta data	c57_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 genes	get_seqs
Gather metadata from KEGG for metabolites	KEGG_gather KEGG_gather.cpd KEGG_gather.KO KEGG_gather.rxn
Get metadata from KEGG API	make_omelette
Perform anova	omu_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 values	omu_summary
Create a PCA plot	PCA_plot
Create a pie chart	pie_chart
plate_omelette Internal method for KEGG_Gather which parses flat text files	plate_omelette plate_omelette.genes plate_omelette.KO plate_omelette.rxn
Clean up orthology metadata	plate_omelette_rxnko
Create a bar plot	plot_bar
Create a box plot	plot_boxplot
Create a heatmap	plot_heatmap
plot_rf_PCA	plot_rf_PCA
plot_variable_importance	plot_variable_importance
Create a volcano plot	plot_volcano
Creates a ratio table from the count_fold_changes function output.	ra_table
random_forest Perform a classification or regression random forest model	random_forest
Import a metabolomics count data frame	read_metabo
transform_metabolites	transform_metabolites
transform_samples	transform_samples