In-house package for metabolome analysis. metapacR is an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted metabolome data. Metabolome results can be imported into metapacR as a numerical matrix, allowing integration into current analysis frameworks. metapacR allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations.
No | Function | Descriptions |
---|---|---|
1 | banner | function to print tidy labels and separators |
2 | boxPlots | function to plot box and violin plot |
3 | compareDiamReduction | funcion to compare different diamentionality reduction methods, namely, PCA, OPLS, TSNE and UMAP |
4 | correlationPlot | function to plot intragroup correlation plot |
5 | diffAbundanceScore | function to analyse differential abundance score of enriched pathways |
6 | distributionPlot | function to analyse distribution of different classes of metabolites |
7 | enrichedNetwork | function to plot enriched annotated netwroks for the signficantly altered metabolic pathways |
8 | enrichedNetwork.KEGG | function to plot influence of metabolic alteration on enriched pathway (direction of change) |
9 | exportResults | function to export results in color coded format in excel table |
10 | findMarkers | function to select and plot most differentiated markers based on roc analysis |
11 | ImputeTransformScale | function to impute, transform and scale raw data |
12 | installScriptLibs | function to install listed R-packages from CRAN and Bioconductor |
13 | leveneStat | function to compute Levene's stats for homogeneity of variance across groups |
14 | lipidChainLengthCorrelation | function to compute correlation of chain length with abundance |
15 | lipidChainLengthDistribution | function to compute distribution of chain length per class |
16 | normalizeDat.binary | function to normalize data using fixed effect as well as mixed effects models for comparison of binary groups ie group vs rest |
17 | normalizeDat | function to normalize data using fixed effect as well as mixed effects models |
18 | piePlot | function to plot pieCharts |
19 | plotDiamReduction | function to plot groups and distribution of metsbolites in diamentionality reduction plot |
20 | plotMarkerViolin | function to plot violin plots of identified markers |
21 | plotMetaboliteAlteration | function to compute atered metabolites distribution per class |
22 | plotSplitViolin | function to plot split violin plots |
23 | rocPlots | function to compute and plot roc curves |
24 | shapiroTest | function to test normality |
25 | volcanoPlots | function to plot volcano plots |
packages <- c("FELLA", "ggtree", "KEGGREST", "ropls")
BiocManager::install(packages)
devtools::install_github("umahajanatlmu/metapacR")