Abstract: | Introduction | Quick Start | Install BNrich | prepare essential data | Unify data, the first step of simplification | BN: construct structures and estimate parameters | construct BN structures | The LASSO regression, the second step of simplification | Estimate the BN parameters | Testing the equality BNs parameters | Variance of BNs parameters | Identification of enriched pathways | Session Info | References:
Package: BNrich 0.1.1
BNrich: Pathway Enrichment Analysis Based on Bayesian Network
Maleknia et al. (2020) <doi:10.1101/2020.01.13.905448>. A novel pathway enrichment analysis package based on Bayesian network to investigate the topology features of the pathways. firstly, 187 kyoto encyclopedia of genes and genomes (KEGG) human non-metabolic pathways which their cycles were eliminated by biological approach, enter in analysis as Bayesian network structures. The constructed Bayesian network were optimized by the Least Absolute Shrinkage Selector Operator (lasso) and the parameters were learned based on gene expression data. Finally, the impacted pathways were enriched by Fisher’s Exact Test on significant parameters.
Authors:
BNrich_0.1.1.tar.gz
BNrich_0.1.1.zip(r-4.7-any)BNrich_0.1.1.zip(r-4.6-any)BNrich_0.1.1.zip(r-4.5-any)
BNrich_0.1.1.tgz(r-4.6-any)BNrich_0.1.1.tgz(r-4.5-any)
BNrich_0.1.1.tar.gz(r-4.7-any)BNrich_0.1.1.tar.gz(r-4.6-any)
BNrich_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BNrich/json (API)
| # Install 'BNrich' in R: |
| install.packages('BNrich', repos = c('https://samaneh-bioinformatics.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/samaneh-bioinformatics/bnrich/issues
networkenrichmentgeneexpressionpathwaysbayesiankegg
Last updated from:8b96e2ced4. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 117 | ||
| source / vignettes | OK | 192 | ||
| linux-release | OK | 125 | ||
| macos-release | OK | 195 | ||
| macos-oldrel | OK | 198 | ||
| windows-devel | OK | 94 | ||
| windows-release | OK | 83 | ||
| windows-oldrel | OK | 95 | ||
| wasm-release | OK | 82 |
Exports:BN_structBNrichesti_parfetch_data_fileLASSO_BNparm_Ttestunify_pathvar_mat
Dependencies:BiocGenericsbnlearncodetoolscorpcorforeachgenericsglmnetgraphiteratorslatticeMatrixRcppRcppEigenshapesurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Construct Bayesian networks structures | BN_struct |
| Analysis of significant final BNs | BNrich |
| Estimate parameters of BNs in control and disease states | esti_par |
| Download data file | fetch_data_file |
| LASSO regression | LASSO_BN |
| Testing the equality regression coefficients | parm_Ttest |
| Simplification networks - applied to unifying nodes | unify_path |
| Estimate variance-covariance matrixes for any parameters of BNs | var_mat |