omu (version 1.1.2)

A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

Description

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.

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Version

Install

install.packages('omu')

Monthly Downloads

296

Version

1.1.2

License

GPL-2

Issues

Pull Requests

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Repository

https://github.com/connor-reid-tiffany/Omu

Homepage

https://www.kegg.jp/kegg/rest/keggapi.html

Maintainer

Connor Tiffany

Last Published

March 6th, 2024

Functions in omu (1.1.2)

Import a metabolomics count data frame

transform_metabolites

ra_table

Creates a ratio table from the count_fold_changes function output.

random_forest

random_forest Perform a classification or regression random forest model

plate_omelette_rxnko

Clean up orthology metadata

KEGG_gather

Gather metadata from KEGG for metabolites

c57_nos2KO_mouse_metadata

c57b6J nos2KO meta data

make_omelette

Get metadata from KEGG API

count_fold_changes

Get counts for significant fold changes by metabolite class.

PCA_plot

Create a PCA plot

get_seqs

Get nucleotide and amino acid sequences for genes

omu_anova

Perform anova

assign_hierarchy

Assign hierarchy metadata

check_zeros

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.

omu_summary

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

plot_volcano

Create a volcano plot

plot_variable_importance

pie_chart

Create a pie chart

plate_omelette

plate_omelette Internal method for KEGG_Gather which parses flat text files

plot_rf_PCA

c57_nos2KO_mouse_countDF

c57b6J nos2KO metabolomics count matrix