TkNA Pipeline

Repository:CAnBioNet/TkNA Tag:v1.2.1 Released by:macovskym

This work was done as a collaboration between Oregon State University and NCI/NIH. Kindly cite the following paper if you use TkNA:
Newman, N.K., Macovsky, M.S., Rodrigues, R.R. et al. Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host–microbiota and other multi-omic interactions. Nat Protoc (2024).

This code performs various tasks related to network reconstruction and analysis, as well as network visualization. It was designed for analyzing microbiome and phenotype data, and the code is organized into five main sections:

1. Network reconstruction: This section reconstructs a network from input data using,, and scripts.

2. Network quality assessment: This section assesses the quality of the reconstructed network using the script.

3. Network analysis: This section analyzes the network, and involves an optional step of generating partitions using either the Louvain algorithm or Infomap, followed by the calculation of network, subnetwork, and node properties using the script.

4. Random network creation and analysis: This section creates random networks and analyzes them to compare their properties to the reconstructed network using,, and scripts.

5. Network visualization: This section visualizes the network using,, and scripts.