Hello,
I want to use Bayesian Network (BN) or Mutual Information (MI) based R packages to construct gene network. I have checked BNArray and CLR, but it seems they are not available on CRAN or Bioconductor, and there is no detailed tutorial to follow, so does anyone know other BN or MI based R packages with available tutorials for gene network construction?
If they are able to identify gene network modules/clusters, it would be best, since my final target is to identify gene clusters/modules.
Thanks in advance.
1 answer
My own tutorial is based on igraph and is actually quite similar to many other published network analysis methods: Network plot from expression data in R using igraph
At least by following that tutorial, you will understand what is happening to your data. With other tools, the process can be heavily automated.
Also, there is a MatLab program called CGBayesnets, written by a colleague of mine.
You are welcome, F
Log in to answer this question.
-
Workflow for functional analysis of differential gene core modules: KEGG, GSEA, and GO enrichment
written by mizzika •
-
Bayesian network for biological data using bnlearn
written by priyankamehta.1811 •
-
Strategies to learn about a gene of interest from single-cell RNA-seq data
written by randalljellis
-
Partial correlation matrix and gene cluster
written by zhang.jianhai •
-
Construct gene coexpression network
written by shuklapriyanka287 •
-
How to model transcriptional networks from gene expression time-course data
written by '
-
Help require for gene regulatory network data
written by mohammad.shaheryar •
-
Identification of master regulator from gene profiles
written by kim •
-
WGCNA implementation for differential co-expression analysis
written by Sathya •
-
Clustering Analysis In Gene Coexpression Network
written by Ane •
If you upload your normalized gene expression data (genes are in rows and samples in columns) in cytoscape, there is network option in menu to infer a regulAtory network by information theory or whatever.hereafter in cytoscape there is a plugin app named moduland by which you can infer interconnected nodes in your network as gene modules.
Thanks for your reply. The Cytoscape may work out, but I want R-based methods since I have many samples and want to write a program to automatically identify gene modules. If I use Cytoscape I have to manually input those samples, and it is not convenient in the long-term.
Minet r package infers the network just by two lines of code. But after building the network easiest way is importing network to cytoscape to use moduland app