Overview | Load OmicNetR | 1. Generate example data | 2. Align samples | 3. Fit sparse CCA | 4. Convert loadings to an interaction network | 5. Visualize results | Bipartite network | Feature importance circle plot | Correlation heatmap | Notes for CRAN
Package: OmicNetR 0.1.1
Prem Prashant Chaudhary
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>).
Authors:
OmicNetR_0.1.1.tar.gz
OmicNetR_0.1.1.tar.gz(r-4.7-any)OmicNetR_0.1.1.tar.gz(r-4.6-any)
OmicNetR_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OmicNetR/json (API)
| # Install 'OmicNetR' in R: |
| install.packages('OmicNetR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- omics_example - Example Multi-Omics Dataset
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:fac20fb185. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 156 | ||
| source / vignettes | OK | 189 | ||
| linux-release-x86_64 | OK | 172 | ||
| wasm-release | OK | 178 |
Exports:align_omicsgenerate_dummy_omicsomic_sccaplot_bipartite_networkplot_correlation_heatmapplot_pathway_circlescca_to_network
Dependencies:clicpp11farverggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMatrixpkgconfigR6RColorBrewerrlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Align Multi-Omic Datasets | align_omics |
| Generate Dummy Multi-Omics Data | generate_dummy_omics |
| Perform Sparse Canonical Correlation Analysis (sCCA) | omic_scca |
| Example Multi-Omics Dataset | omics_example |
| Plot Bi-partite sCCA Weight Network | plot_bipartite_network |
| Global Gene-Metabolite Correlation Heatmap | plot_correlation_heatmap |
| Canonical Loading Pathway Circle Plot | plot_pathway_circle |
| Convert sCCA Loadings to Network Edges | scca_to_network |