Comments (1)
Hi,
The package is generally applicable to any kind of count data, and especially to data where compositionality is an issue. In NetCoMi, the rows and columns are called samples and taxa because it was designed for microbiome data. However, it can also be used to generate gene-gene networks, for example. To estimate associations, you could use, e.g., the SPRING approach, or follow standard RNA-seq pipelines and pass the association matrix directly to the netConstruct function.
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Related Issues (20)
- output format for Gephi visualization HOT 2
- Colored by phylum HOT 2
- stability values using spieceasi HOT 1
- Problems while installing the NetCoMi HOT 1
- How to find a "good" algorithm and parameter set HOT 1
- Error in length of dimnames after permutation testing HOT 1
- Labelling only certain taxa of interest HOT 1
- Will this package works for all lineage levels?
- Cross domain interactions HOT 3
- calculate the betweenness centrality as hubs HOT 2
- Looking for guidance on MANs Inference with samples from different metagenomics/metatranscriptomics studies HOT 4
- Error in NetConstruct for network comparison : "subscript out of bounds" HOT 4
- edges dont color correctly with negative correlations HOT 2
- Could I manually modify the color of each node? HOT 2
- Problem with the targets IDs in export to gephi HOT 4
- including correlations with environmental or experimental variables? HOT 3
- Understanding netConstruct() output HOT 1
- Issue with node size and netCompare HOT 5
- How to easily understand the GCM heatmap
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