Man pages for montilab/bieulergy
Interactive analysis of multi-omics regulatory networks
| cfx | Color ramp functions |
| colorize | Colorize numerical values |
| colorize.heat | Colorize numerical values for the heat palette |
| create.ionet | Create interactive omics network objects |
| create.ionets | Create a list of interactive omics network objects |
| ggempty | An empty ggplot |
| ggeplot | Enrichment plot implemented in ggplot |
| ggwrs | Weighted rank scores plot implement in ggplot |
| ig | centrality |
| ig.assortivity | Graph-level assortivity |
| ig.betweeness | Node-level betweeness centrality |
| ig.centrality | Functions for calculating node-level centrality measures |
| ig.clustering | Graph-level clustering |
| ig.components | Graph-level components |
| ig.create | Helper function for creating graph objects |
| ig.dangalchev | Node-level dangalchev closeness centrality |
| ig.degree | Node-level degree centrality |
| ig.density | Graph-level density |
| ig.diameter | Graph-level diameter |
| ig.diffusion | Node-level diffusion centrality |
| ig.eccentricity | Node-level eccentricity centrality |
| ig.edges | Graph-level edge count |
| ig.efficiency | Graph-level efficiency |
| ig.eigen | Node-level eigenvector centrality |
| ig.isolated | Graph-level isolated |
| ig.katz | Node-level katz centrality |
| ig.laplacian | Node-level laplacian centrality |
| ig.leverage | Node-level leverage centrality |
| ig.nodes | Graph-level vertex count |
| ig.properties | Functions for calculating graph-level properties |
| ig.rwr | Random walk with restart |
| ig.stress | Node-level stress centrality |
| ig.topoco | Node-level topological coefficient centrality |
| ig.to.vn | Convert ig to vn |
| ig.transitivity | Graph-level transitivity |
| interactive.omics.network | Interaction Omics Network Object |
| is.ionet | Check if object is an interactive omics network objects |
| is.network | Checks if object is a interactive omics network object |
| is.networks | Checks if object is a list of interactive omics network... |
| kstest | Two-sided Kolmogorov–Smirnov test |
| network.kstest | Centrality-based enrichment |
| network.pca.contri | PCA - Contibutors |
| network.pca.hclust | PCA - Hierarchical Clustering |
| network.pca.pltvar | PCA - Show Contributors |
| network.pca.varexp | PCA - Variance Explained |
| networks.cdistr | Centrality distributions |
| networks.diffc | Differential Centrality Rankings Across Networks |
| networks.hclust | Hierarchical Clustering of Networks by Centrality |
| networks.tnodes | Important Nodes |
| normalize.nlog | Normalize significance values |
| normalize.nlog.range | Normalize significance values between a given range |
| normalize.range | Normalize values between a given range |
| normalize.zo | Normalize values between zero and one |
| pseudo.log.trans | Pseudo-log transformation |
| pseudo.log.trans.rev | Pseudo-log transformation in reverse |
| rcolors | Repeatable vector of distinct colors |
| run.shiny | Spin up an instance of the shiny application |
| theme_simplex | An ggplot theme for simplex applications |
| vn.to.ig | Convert vn to ig |
