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knitr::opts_chunk$set( collapse = TRUE, comment = “#>”, fig.path = “man/figures/README-”, out.width = “100%” )

Load the LOCAL package during knitting

devtools::load_all()

##OmicNetR

#OmicNetR is an R package for the integrated analysis of multi-omics datasets using Sparse Canonical Correlation Analysis (sCCA).

#Installation

#You can install the development version of OmicNetR from GitHub:

install.packages(“devtools”)

devtools::install_github(“ppchaudhary/OmicNetR”)

#Quick Start Example

#This example demonstrates how to generate integrated networks and importance plots.

library(OmicNetR)

1. Generate synthetic data

set.seed(123) data <- generate_dummy_omics( n_samples = 60, n_genes = 800, n_metabolites = 150 )

2. Run sCCA

scca_model <- omic_scca( data\(X, data\)Y, penalty_X = 0.7, penalty_Y = 0.7 )

3. Plot bipartite network

net_data <- scca_to_network( scca_model, weight_threshold = 0.05 ) plot_bipartite_network(net_data)

4. Plot circular importance

plot_pathway_circle( scca_model, top_features = 30 )

Biological Interpretation

Nodes

Blue circles represent genes

Orange circles represent metabolites

Edges

Green lines indicate positive correlations

Red lines indicate negative correlations

Contact

Developed by Prem Prashant Chaudhary GitHub ID: ppchaudhary

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.