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OmicFlow (version 1.4.2)

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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Version

Install

install.packages('OmicFlow')

Monthly Downloads

450

Version

1.4.2

License

MIT + file LICENSE

Issues

4

Pull Requests

0

Stars

1

Forks

0

Maintainer

Alem Gusinac

Last Published

November 30th, 2025

Functions in OmicFlow (1.4.2)

pairwise_adonis

Pairwise adonis2 (PERMANOVA) computation
metagenomics

Sub-class metagenomics
jaccard

Compute Jaccard Dissimilarity from a Sparse Matrix.
pairwise_anosim

Pairwise anosim (ANOSIM) computation
hill_taxa

Sparse implementation of Hill numbers
omics

Abstract omics class
ordination_plot

Ordination plot
jsd

Compute Jensen-Shannon Divergence from a Sparse Matrix.
plot_pairwise_stats

Create pairwise stats plot
manhattan

Compute Manhattan Dissimilarity from a Sparse Matrix.
proteomics

Sub-class proteomics
sparse_to_dtable

Converting a sparse matrix to data.table
volcano_plot

Volcano plot
read_rarefraction_qiime

Loads a rarefied alpha diversity table from Qiime2
unifrac

Compute UniFrac Dissimilarity from a Sparse Matrix.
colormap

Color map of a variable
column_exists

Checks if column exists in table
cosine

Compute Cosine Dissimilarity from a Sparse Matrix.
composition_plot

Compositional plot
diversity

Sparse implementation of Alpha Diversity Metrics
canberra

Compute Canberra Dissimilarity from a Sparse Matrix.
OmicFlow-package

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

Compute Bray-Curtis Dissimilarity from a Sparse Matrix.
diversity_plot

Diversity plot
foldchange

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