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OmicFlow (version 1.4.0)

Fast and Efficient (Automated) Analysis of Sparse Omics Data

Description

A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user, which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class. Once this unified structure is established, users can perform manual subsetting, visualisation, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.

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Install

install.packages('OmicFlow')

Monthly Downloads

450

Version

1.4.0

License

MIT + file LICENSE

Issues

4

Pull Requests

0

Stars

1

Forks

0

Maintainer

Alem Gusinac

Last Published

October 29th, 2025

Functions in OmicFlow (1.4.0)

ordination_plot

Ordination plot
manhattan

Compute Manhattan Dissimilarity from a Sparse Matrix.
plot_pairwise_stats

Create pairwise stats plot
omics

Abstract omics class
pairwise_anosim

Pairwise anosim (ANOSIM) computation
pairwise_adonis

Pairwise adonis2 (PERMANOVA) computation
volcano_plot

Volcano plot
jaccard

Compute Jaccard Dissimilarity from a Sparse Matrix.
hill_taxa

Sparse implementation of Hill numbers
sparse_to_dtable

Converting a sparse matrix to data.table
metagenomics

Sub-class metagenomics
proteomics

Sub-class proteomics
unifrac

Compute UniFrac Dissimilarity from a Sparse Matrix.
read_rarefraction_qiime

Loads a rarefied alpha diversity table from Qiime2
composition_plot

Compositional plot
canberra

Compute Canberra Dissimilarity from a Sparse Matrix.
column_exists

Checks if column exists in table
foldchange

Computes Log2(A) - Log2(B) Fold Change of (non-) paired data.
diversity_plot

Diversity plot
bray

Compute Bray-Curtis Dissimilarity from a Sparse Matrix.
colormap

Color map of a variable
cosine

Compute Cosine Dissimilarity from a Sparse Matrix.
diversity

Sparse implementation of Alpha Diversity Metrics
OmicFlow-package

OmicFlow: Fast and Efficient (Automated) Analysis of Sparse Omics Data
jsd

Compute Jensen-Shannon Divergence from a Sparse Matrix.