OmicNetR
Network-Based Integration of Multi-Omics Data Using Sparse CCA
Provides an end-to-end workflow for integrative analysis of two omics layers using sparse canonical correlation analysis (sCCA), including sample alignment, feature selection, network edge construction, and visualization of gene-metabolite relationships. The underlying methods are based on penalized matrix decomposition and sparse CCA (Witten, Tibshirani and Hastie (2009) <doi:10.1093/biostatistics/kxp008>), with design principles inspired by multivariate integrative frameworks such as mixOmics (Rohart et al. (2017) <doi:10.1371/journal.pcbi.1005752>).
README
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
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
0.1.1 |
rolling linux/jammy R-4.5 | OmicNetR_0.1.1.tar.gz |
1.0 MiB |
0.1.1 |
rolling linux/noble R-4.5 | OmicNetR_0.1.1.tar.gz |
1.0 MiB |
0.1.1 |
rolling source/ R- | OmicNetR_0.1.1.tar.gz |
1.0 MiB |
0.1.1 |
latest linux/jammy R-4.5 | OmicNetR_0.1.1.tar.gz |
1.0 MiB |
0.1.1 |
latest linux/noble R-4.5 | OmicNetR_0.1.1.tar.gz |
1.0 MiB |
0.1.1 |
latest source/ R- | OmicNetR_0.1.1.tar.gz |
1.0 MiB |
0.1.1 |
2026-04-26 source/ R- | OmicNetR_0.1.1.tar.gz |
1.0 MiB |
0.1.1 |
2026-04-23 source/ R- | OmicNetR_0.1.1.tar.gz |
1.0 MiB |
0.1.1 |
2026-04-09 windows/windows R-4.5 | OmicNetR_0.1.1.zip |
1.0 MiB |