zhiqianx
commented
1 year ago Notes about NetBoxR https://github.com/mil2041/netboxr/tree/master
- Run through an interactive R session
- Require R 4.1.0, Bioconductor 3.14, created an environment for that
- Dependency ggtree require R 4.3 with Bioconductor 3.17
- a lot of modifications on my environment and local machine to make it run
- Long package downloading time
What does it do?
- use NetBox algorithm to identify candidate cancer-related functional modules
- network-based approach that combines prior knowledge with a network clustering algorithm allows for the identification of functional modules
Package and libraries needed for the method
- R
- Igraph
- parallel
Input for the method
- network = .sif file
- gene list = .txt file -> “significantly” altered genes
- or can be load from .rda file
Output of the method
- network.sif
- sif file in format: NODE1 INTERACTION_TYPE NODE2
Other Functions
- Plot graph for the output network
- Check statistical significance of the discovered network & draw histogram to show
- view module membership -> the intramodular connectivity of any gene in a given module
- Other output can be generate:
- netighborList.txt = the information of all neighbor nodes
- community.membership.txt = indicates the identified pathway module numbers
- nodeType.txt = tell the node is 'linker' node or 'candidate' node.
agitter
Automated Network Analysis Identifies Core Pathways in Glioblastoma https://doi.org/10.1371/journal.pone.0008918
The original implementation from http://sanderlab.org/tools/netbox.html is no longer available. In our pathway parameter advising repository we link to http://cbio.mskcc.org/wp-content/uploads/2012/10/netbox.tar.gz and note it has been replaced by the NetBoxR R package at https://www.bioconductor.org/packages/release/bioc/html/netboxr.html.