PTMsToPathways: Filtered CoCluster Correlation Network Guide — PTMsToPathways • PTMsToPathways

PTMsToPathways provides tools for turning mass spectrometry data on post-translational modifications into clustered networks, co-cluster correlation networks, and downstream pathway and Cytoscape-ready views. The package includes example PTM tables, BRCA example networks, and helper functions for building CCCNs, cluster-filtered PPIs, and pathway crosstalk networks.

Details

Typical entry points are MakeClusterList(), MakeCorrelationNetwork(), BuildClusterFilteredNetwork(), BuildPathwayCrosstalkNetwork(), and the Cytoscape helpers in GraphCfn() and related functions.

The package comes with many example datasets that can be seen in the vignettes.

See also

utils::browseVignettes()

Author

Maintainer: Lucia Williams lucia.williams@umt.edu (ORCID)

Authors:

Lucia Williams lucia.williams@umt.edu (ORCID)
Mark Grimes (ORCID)
Mikhail Ukrainetz
Grant Smith
Madison Moffett
Nagashree Avabhrath