CoNet - Supplemental material for cross-biome analysis
Here is the supplemental material for the cross-biome analysis with CoNet, published in
Frontiers in Microbiology.
We constructed networks for 20 biome-specific data sets, which we obtained from
the QIIME and EMP databases.
The original 16S count data and metadata are available from these databases, filtered data after processing
is available from the Data section of CoNet.
A Cytoscape cys file with all 20 networks can be downloaded here.
The networks can be reconstructed with CoNet on command line using this bash script.
For network construction with CoNet in Cytoscape, you can use this settings file to generate
permutations and this settings file to generate bootstraps and the final network.
To simulate count matrices and carry out network construction in R, use this R script.